variant matrix strand/coding/non-coding bug

Each locus ID should get a strand information seperately
If one gene is coding and another is non-coding => Coding + Non-coding
ERROR_OUT_OF_CHROMOSOME_RANGE snp eff debugging. Make changes in matrix for this instances

When these is present in the row annotation --  ERROR_OUT_OF_CHROMOSOME_RANGE or locus_tag to CHR_END --
change annotation to make the variant intergenic between the first and last gene of the chromosome.

Non-coding SNP at 4293521 > T,C,G functional=NULL_NULL_NULL locus_tag= strand=Null;
G||MODIFIER|||||||ERROR_OUT_OF_CHROMOSOME_RANGE||ERROR_OUT_OF_CHROMOSOME_RANGE;T||
MODIFIER|||||||ERROR_OUT_OF_CHROMOSOME_RANGE||ERROR_OUT_OF_CHROMOSOME_RANGE;C||MODIFIER
|||||||ERROR_OUT_OF_CHROMOSOME_RANGE||ERROR_OUT_OF_CHROMOSOME_RANGE;
Non-coding SNP at 4290130 > C functional=NULL_NULL_NULL locus_tag=CD630_36800 strand=-;
C|intergenic_region|MODIFIER|rpmH-CHR_END|n.4290130A>C||||rpmH|null or hypothetical protein;

Need strand information if a position is in two genes (that is, overlapping genes) because the genes
could be on different strand

Non-coding SNP at 455792 > A,C functional=NULL_NULL_NULL locus_tag=CD630_03860 strand=-;A|
intron_variant|MODIFIER|CD630_03540|c.31-1213T>A||||CD630_03540|CD630_03540;C|
intron_variant|MODIFIER|CD630_03540|c.31-1213T>C||||CD630_03540|CD630_03540;C|synonymous_variant|
LOW|CD630_03860|c.819A>G|p.Val273Val|819/3045|273/1014|CD630_03860|CD630_03860;”

If one variant is in a non-coding region (intergenic, intron) and the other is in a coding region, we want
to know that information. For example: mutation in CD630_03860 is coding, but it says non-coding because of
the intron variant

Non-coding SNP at 455792 > A,C functional=NULL_NULL_NULL locus_tag=CD630_03860 strand=-;A|
intron_variant|MODIFIER|CD630_03540|c.31-1213T>A||||CD630_03540|CD630_03540;C|
intron_variant|MODIFIER|CD630_03540|c.31-1213T>C||||CD630_03540|CD630_03540;C|synonymous_variant|
LOW|CD630_03860|c.819A>G|p.Val273Val|819/3045|273/1014|CD630_03860|CD630_03860;”

There is some bug producing brackets contained ###:### after the strand information in certain row annotations
Coding SNP at 2093672 > G functional=NULL_NULL_NULL locus_tag=CD630_18090 strand=+,
[2092758:2093730];G|missense_variant|MODERATE|CD630_18090|c.1112T>G|p.Met371Arg|1112/1170|371/389|
null or hypothetical protein|Fragment of putative permease, MFS family;

In both the new snp mat (including the outgroup) and the old snp mat (no outgroup) when the SNP has two alleles (ex: > A, C) a Coding SNP is incorrectly called as a non-coding SNP. See for example below:
The SNP mat that includes the outgroup has the following row:
"Non-coding SNP at 195 > A,C functional=NULL_NULL_NULL locus_tag=CD630_00010 strand=+;A|synonymous_variant|LOW|CD630_00010|c.195T>A|p.Ile65Ile|195/1320|65/439|dnaA|dnaA;C|synonymous_variant|LOW|CD630_00010|c.195T>C|p.Ile65Ile|195/1320|65/439|dnaA|dnaA;”
It seems to me that this variant should be classified as a Coding SNP, right? It’s within the gene dnaA.
In the SNP mat that does not include the outgroup the same position is classified as a Coding SNP:
"Coding SNP at 195 > C functional=NULL_NULL_NULL locus_tag=CD630_00010 strand=+;C|synonymous_variant|LOW|dnaA|c.195T>C|p.Ile65Ile|195/1320|65/439|dnaA|null or hypothetical protein;"
Have you seen behavior like that before? Any guesses why the first variant is misclassified as a non-coding SNP?
I was able to find examples of the same behavior within the old SNP mat. See this example:
"Non-coding SNP at 16983 > A,G functional=NULL_NULL_NULL locus_tag=CD630_00130 strand=+;G|synonymous_variant|LOW|CD630_00130|c.372T>G|p.Ser124Ser|372/882|124/293|CD630_00130|CD630_00130;A|synonymous_variant|LOW|CD630_00130|c.372T>A|p.Ser124Ser|372/882|124/293|CD630_00130|CD630_00130;"

Related bug:
Here is the variant from the SNP matrix prior to including the outgroup:
[1] "Coding SNP at 61673 > C functional=NULL_NULL_NULL locus_tag=CD630_00390 strand=+;C|synonymous_variant|LOW|acoL|c.15A>C|p.Val5Val|15/1731|5/576|acoL|null or hypothetical protein;"
Here is the variant from the SNP matrix after including the outgroup:
[1] "Non-coding SNP at 61673 > T,C functional=NULL_NULL_NULL locus_tag=CD630_00380-CD630_00390 strand=+/+/;T|synonymous_variant|LOW|CD630_00390|c.15A>T|p.Val5Val|15/1731|5/576|acoL|acoL;C|synonymous_variant|LOW|CD630_00390|c.15A>C|p.Val5Val|15/1731|5/576|acoL|acoL;"
The difference is that in the no-outgroup-matrix the position is considered within a gene but in the yes-outgroup-matrix the position is considered intergenic. Which is correct?

Noticed odd behavior:
SNP in no-outgroup-matrix:
"Non-coding SNP at 294446 > C functional=NULL_NULL_NULL locus_tag=CD630_02280-CD630_02290 strand=+/+/;C|intergenic_region|MODIFIER|fliN-flgM|n.294446T>C||||fliN,flgM|Flagellar motor switch protein FliN,Negative regulator of flagellin synthesis (Anti-sigma-d factor),;"
SNP in yes-outgroup-matrix:
"Non-coding SNP at 294446 > A,C functional=NULL_NULL_NULL locus_tag=CD630_02280 strand=+;A|intergenic_region|MODIFIER|CD630_02280-CD630_02290|n.294446T>A||||fliN-flgM|fliN-flgM;C|intergenic_region|MODIFIER|CD630_02280-CD630_02290|n.294446T>C||||fliN-flgM|fliN-flgM;"
Even though the SNP is classified as intergenic in both matrices and the two gene names are present in both matrices, in the yes-outgroup-matrix the locus_tag only has one ID instead of two IDs with a dash. The locus_tag is correct in the no-outgroup-matrix. It looks like the gene names (fliN and fliM) are used the no-outgroup-matrix but the locus_tag is used in the yes-outgroup-matrix.

In this yes-outgroup-matrix variant no annotation was included, but the annotation is included in the no-outgroup-matrix. Instead of the annotation the information is just the two locus tags repeatedly.
no_outgroup
"Non-coding SNP at 370354 > C functional=NULL_NULL_NULL locus_tag=CD630_03080-CD630_03090 strand=+, [369999:370059]/-/;C|intergenic_region|MODIFIER|CD630_03080-CD630_03090|n.370354T>C||||null or hypothetical protein,null or hypothetical protein|null or hypothetical protein,putative hydrolase, HAD superfamily, subfamily IB,;"
yes outgroup:
"Non-coding SNP at 370354 > G,C functional=NULL_NULL_NULL locus_tag=CD630_03080 strand=+, [369999:370059];G|intergenic_region|MODIFIER|CD630_03080-CD630_03090|n.370354T>G||||CD630_03080-CD630_03090|CD630_03080-CD630_03090;C|intergenic_region|MODIFIER|CD630_03080-CD630_03090|n.370354T>C||||CD630_03080-CD630_03090|CD630_03080-CD630_03090;"

For this variant, in addition to the locus tag only having one of the two necessary locus tags the annotations are replaced with the gene sympbols in the yes-outgroup-matrix.
                                                                                No-outgroup
                              "Non-coding SNP at 403794 > G functional=NULL_NULL_NULL locus_tag=CD630_03330-CD630_03340 strand=-/+/;G|intergenic_region|MODIFIER|ppaC-adhE|n.403794A>G||||ppaC,adhE|putative inorganic pyrophosphatase,null or hypothetical protein,;"
                                                                                Yes-outgroup

"Non-coding SNP at 403794 > T,G functional=NULL_NULL_NULL locus_tag=CD630_03330 strand=-;G|intergenic_region|MODIFIER|CD630_03330-CD630_03340|n.403794A>G||||ppaC-adhE|ppaC-adhE;T|intergenic_region|MODIFIER|CD630_03330-CD630_03340|n.403794A>T||||ppaC-adhE|ppaC-adhE;"

For this variant the missense and synonymous mutations in the yes-outgroup-matrix have this message: "WARNING_TRANSCRIPT_NO_START_CODON". I found that this phrase also occurs in ~1200 variants in the no-outgroup-matrix as well.
No-outgroup-matrix.
"Coding SNP at 428498 > G functional=NULL_NULL_NULL locus_tag=CD630_03541 strand=+, [428257:428326];G|intron_variant|MODIFIER|CD630_03540|c.30+394T>G||||null or hypothetical protein|Fragment of putative membrane protein;G|missense_variant|MODERATE|CD630_03541|c.388T>G|p.Leu130Val|388/567|130/188|null or hypothetical protein|null or hypothetical protein;"
Yes-outgroup-matrix:
"Non-coding SNP at 428498 > C,G functional=NULL_NULL_NULL locus_tag=CD630_03540 strand=+, [457004:457163];G|missense_variant|MODERATE|CD630_03541|c.388T>G|p.Leu130Val|388/567|130/188||WARNING_TRANSCRIPT_NO_START_CODON||WARNING_TRANSCRIPT_NO_START_CODON;C|intron_variant|MODIFIER|CD630_03540|c.30+394T>C||||CD630_03540|CD630_03540;C|synonymous_variant|LOW|CD630_03541|c.388T>C|p.Leu130Leu|388/567|130/188||WARNING_TRANSCRIPT_NO_START_CODON||WARNING_TRANSCRIPT_NO_START_CODON;"

For this variant there are two different locus tags for the same position in both the no-outgroup-matrix and the yes-outgroup-matrix. I think there is an issue with it being an intron?
428665 is assigned to locus-tag CD630_03540 and CD630_03541 in both matrices.
no outgroup:
"Non-coding SNP at 428665 > C,T functional=NULL_NULL_NULL locus_tag=CD630_03540 strand=+, [457004:457163];C|synonymous_variant|LOW|CD630_03541|c.555A>C|p.Ile185Ile|555/567|185/188||WARNING_TRANSCRIPT_NO_START_CODON||WARNING_TRANSCRIPT_NO_START_CODON;C|intron_variant|MODIFIER|CD630_03540|c.30+561A>C||||CD630_03540|CD630_03540;T|synonymous_variant|LOW|CD630_03541|c.555A>T|p.Ile185Ile|555/567|185/188||WARNING_TRANSCRIPT_NO_START_CODON||WARNING_TRANSCRIPT_NO_START_CODON;"
yes outgroup:
"Non-coding SNP at 428665 > C,T functional=NULL_NULL_NULL locus_tag=CD630_03541 strand=+, [428257:428326];C|synonymous_variant|LOW|CD630_03541|c.555A>C|p.Ile185Ile|555/567|185/188||WARNING_TRANSCRIPT_NO_START_CODON||WARNING_TRANSCRIPT_NO_START_CODON;C|intron_variant|MODIFIER|CD630_03540|c.30+561A>C||||CD630_03540|CD630_03540;T|synonymous_variant|LOW|CD630_03541|c.555A>T|p.Ile185Ile|555/567|185/188||WARNING_TRANSCRIPT_NO_START_CODON||WARNING_TRANSCRIPT_NO_START_CODON;"

Similar to the previous issue, the yes_outgroup_matrix maps to two different loci, only one of which matches the locus_tag in the no-outgroup-matrix. This time, though, introns don't appear to play a part.
no outgroup
"Coding SNP at 473543 > C functional=NULL_NULL_NULL locus_tag=CD630_04010 strand=+;C|synonymous_variant|LOW|etfA1|c.87A>C|p.Ile29Ile|87/1038|29/345|etfA1|null or hypothetical protein;"
yes outgroup
"Non-coding SNP at 473543 > T,C functional=NULL_NULL_NULL locus_tag=CD630_04000 strand=+;C|synonymous_variant|LOW|CD630_04010|c.87A>C|p.Ile29Ile|87/1038|29/345|etfA1|etfA1;T|synonymous_variant|LOW|CD630_04010|c.87A>T|p.Ile29Ile|87/1038|29/345|etfA1|etfA1;"

The yes-outgroup variant has two locus tags (instead of just one) and has brackets whic are not found in no-outgroup variant.
no outgroup
"Coding SNP at 607587 > T functional=NULL_NULL_NULL locus_tag=CD630_05140 strand=+;T|synonymous_variant|LOW|cwpV|c.27A>T|p.Ala9Ala|27/4869|9/1622|cwpV|putative hemagglutinin/adhesin cwpV;"
yes outgroup
"Non-coding SNP at 607587 > C,T functional=NULL_NULL_NULL locus_tag=CD630_05130-CD630_05140 strand=+, [606702:606756]/+/;T|synonymous_variant|LOW|CD630_05140|c.27A>T|p.Ala9Ala|27/4869|9/1622|cwpV|cwpV;C|synonymous_variant|LOW|CD630_05140|c.27A>C|p.Ala9Ala|27/4869|9/1622|cwpV|cwpV;"

Locus tag is in many positions for no outgroup (is gene symbol and annotation missing? does it not exist?)
"Non-coding SNP at 747059 > A,T functional=NULL_NULL_NULL locus_tag=CD630_06250-CD630_06260 strand=+/+/;A|intergenic_region|MODIFIER|CD630_06250-CD630_06260|n.747059G>A||||CD630_06250-CD630_06260|CD630_06250-CD630_06260;T|intergenic_region|MODIFIER|CD630_06250-CD630_06260|n.747059G>T||||CD630_06250-CD630_06260|CD630_06250-CD630_06260;"

In both the new snp mat (including the outgroup) and the old snp mat (no outgroup) when the SNP has two alleles (ex: > A, C) a Coding SNP is incorrectly called as a non-coding SNP. See for example below:
The SNP mat that includes the outgroup has the following row:
"Non-coding SNP at 195 > A,C functional=NULL_NULL_NULL locus_tag=CD630_00010 strand=+;A|synonymous_variant|LOW|CD630_00010|c.195T>A|p.Ile65Ile|195/1320|65/439|dnaA|dnaA;C|synonymous_variant|LOW|CD630_00010|c.195T>C|p.Ile65Ile|195/1320|65/439|dnaA|dnaA;”
It seems to me that this variant should be classified as a Coding SNP, right? It’s within the gene dnaA.
In the SNP mat that does not include the outgroup the same position is classified as a Coding SNP:
"Coding SNP at 195 > C functional=NULL_NULL_NULL locus_tag=CD630_00010 strand=+;C|synonymous_variant|LOW|dnaA|c.195T>C|p.Ile65Ile|195/1320|65/439|dnaA|null or hypothetical protein;"
Have you seen behavior like that before? Any guesses why the first variant is misclassified as a non-coding SNP?
I was able to find examples of the same behavior within the old SNP mat. See this example:
"Non-coding SNP at 16983 > A,G functional=NULL_NULL_NULL locus_tag=CD630_00130 strand=+;G|synonymous_variant|LOW|CD630_00130|c.372T>G|p.Ser124Ser|372/882|124/293|CD630_00130|CD630_00130;A|synonymous_variant|LOW|CD630_00130|c.372T>A|p.Ser124Ser|372/882|124/293|CD630_00130|CD630_00130;"

This bug is fixed.

Related bug:
Here is the variant from the SNP matrix prior to including the outgroup:
[1] "Coding SNP at 61673 > C functional=NULL_NULL_NULL locus_tag=CD630_00390 strand=+;C|synonymous_variant|LOW|acoL|c.15A>C|p.Val5Val|15/1731|5/576|acoL|null or hypothetical protein;"
Here is the variant from the SNP matrix after including the outgroup:
[1] "Non-coding SNP at 61673 > T,C functional=NULL_NULL_NULL locus_tag=CD630_00380-CD630_00390 strand=+/+/;T|synonymous_variant|LOW|CD630_00390|c.15A>T|p.Val5Val|15/1731|5/576|acoL|acoL;C|synonymous_variant|LOW|CD630_00390|c.15A>C|p.Val5Val|15/1731|5/576|acoL|acoL;"
The difference is that in the no-outgroup-matrix the position is considered within a gene but in the yes-outgroup-matrix the position is considered intergenic. Which is correct?

Cannot reproduce this bug. This position is suppose to have only one variant - "T". In the new matrix that includes, this is fixed.

294446

This is fixed. Considering it is in intergenic region it should not contain product name information. Also, it now contains bothe the locus IDs in row annotation.

Noticed odd behavior:
SNP in no-outgroup-matrix:
"Non-coding SNP at 294446 > C functional=NULL_NULL_NULL locus_tag=CD630_02280-CD630_02290 strand=+/+/;C|intergenic_region|MODIFIER|fliN-flgM|n.294446T>C||||fliN,flgM|Flagellar motor switch protein FliN,Negative regulator of flagellin synthesis (Anti-sigma-d factor),;"
SNP in yes-outgroup-matrix:
"Non-coding SNP at 294446 > A,C functional=NULL_NULL_NULL locus_tag=CD630_02280 strand=+;A|intergenic_region|MODIFIER|CD630_02280-CD630_02290|n.294446T>A||||fliN-flgM|fliN-flgM;C|intergenic_region|MODIFIER|CD630_02280-CD630_02290|n.294446T>C||||fliN-flgM|fliN-flgM;"
Even though the SNP is classified as intergenic in both matrices and the two gene names are present in both matrices, in the yes-outgroup-matrix the locus_tag only has one ID instead of two IDs with a dash. The locus_tag is correct in the no-outgroup-matrix. It looks like the gene names (fliN and fliM) are used the no-outgroup-matrix but the locus_tag is used in the yes-outgroup-matrix.

This is fixed. Considering it is in intergenic region it should not contain product name information. Also, it now contains bothe the locus IDs in row annotation.

In this yes-outgroup-matrix variant no annotation was included, but the annotation is included in the no-outgroup-matrix. Instead of the annotation the information is just the two locus tags repeatedly.
no_outgroup
"Non-coding SNP at 370354 > C functional=NULL_NULL_NULL locus_tag=CD630_03080-CD630_03090 strand=+, [369999:370059]/-/;C|intergenic_region|MODIFIER|CD630_03080-CD630_03090|n.370354T>C||||null or hypothetical protein,null or hypothetical protein|null or hypothetical protein,putative hydrolase, HAD superfamily, subfamily IB,;"
yes outgroup:
"Non-coding SNP at 370354 > G,C functional=NULL_NULL_NULL locus_tag=CD630_03080 strand=+, [369999:370059];G|intergenic_region|MODIFIER|CD630_03080-CD630_03090|n.370354T>G||||CD630_03080-CD630_03090|CD630_03080-CD630_03090;C|intergenic_region|MODIFIER|CD630_03080-CD630_03090|n.370354T>C||||CD630_03080-CD630_03090|CD630_03080-CD630_03090;"

This fixed:
Non-Coding SNP at 370354 > G functional=NULL_NULL_NULL locus_tag=CD630_03080-CD630_03090 Strand Information: CD630_03080=+/CD630_03090=-/;G|intergenic_region|MODIFIER|CD630_03080-CD630_03090|n.370354T>G||||null or hypothetical protein,null or hypothetical protein,|null or hypothetical protein,putative hydrolase, HAD superfamily, subfamily IB,;

For this variant, in addition to the locus tag only having one of the two necessary locus tags the annotations are replaced with the gene sympbols in the yes-outgroup-matrix.
                                                                                No-outgroup
                              "Non-coding SNP at 403794 > G functional=NULL_NULL_NULL locus_tag=CD630_03330-CD630_03340 strand=-/+/;G|intergenic_region|MODIFIER|ppaC-adhE|n.403794A>G||||ppaC,adhE|putative inorganic pyrophosphatase,null or hypothetical protein,;"
                                                                                Yes-outgroup

"Non-coding SNP at 403794 > T,G functional=NULL_NULL_NULL locus_tag=CD630_03330 strand=-;G|intergenic_region|MODIFIER|CD630_03330-CD630_03340|n.403794A>G||||ppaC-adhE|ppaC-adhE;T|intergenic_region|MODIFIER|CD630_03330-CD630_03340|n.403794A>T||||ppaC-adhE|ppaC-adhE;"

This position is suppose to have only one variant - "T". I could reproduce the error but this seems to be fixed. If its not, please comment:
Non-Coding SNP at 403794 > T functional=NULL_NULL_NULL locus_tag=CD630_03330-CD630_03340 Strand Information: CD630_03330=-/CD630_03340=+/;T|intergenic_region|MODIFIER|ppaC-adhE|n.403794A>T||||ppaC,adhE,|putative inorganic pyrophosphatase,null or hypothetical protein,;

For this variant the missense and synonymous mutations in the yes-outgroup-matrix have this message: "WARNING_TRANSCRIPT_NO_START_CODON". I found that this phrase also occurs in ~1200 variants in the no-outgroup-matrix as well.
No-outgroup-matrix.
"Coding SNP at 428498 > G functional=NULL_NULL_NULL locus_tag=CD630_03541 strand=+, [428257:428326];G|intron_variant|MODIFIER|CD630_03540|c.30+394T>G||||null or hypothetical protein|Fragment of putative membrane protein;G|missense_variant|MODERATE|CD630_03541|c.388T>G|p.Leu130Val|388/567|130/188|null or hypothetical protein|null or hypothetical protein;"
Yes-outgroup-matrix:
"Non-coding SNP at 428498 > C,G functional=NULL_NULL_NULL locus_tag=CD630_03540 strand=+, [457004:457163];G|missense_variant|MODERATE|CD630_03541|c.388T>G|p.Leu130Val|388/567|130/188||WARNING_TRANSCRIPT_NO_START_CODON||WARNING_TRANSCRIPT_NO_START_CODON;C|intron_variant|MODIFIER|CD630_03540|c.30+394T>C||||CD630_03540|CD630_03540;C|synonymous_variant|LOW|CD630_03541|c.388T>C|p.Leu130Leu|388/567|130/188||WARNING_TRANSCRIPT_NO_START_CODON||WARNING_TRANSCRIPT_NO_START_CODON;"

snpEff outputs a warning in outgroup sample. I will remove this warning from the row annotation. Needs fixing.

428665

For this variant there are two different locus tags for the same position in both the no-outgroup-matrix and the yes-outgroup-matrix. I think there is an issue with it being an intron?
428665 is assigned to locus-tag CD630_03540 and CD630_03541 in both matrices.
no outgroup:
"Non-coding SNP at 428665 > C,T functional=NULL_NULL_NULL locus_tag=CD630_03540 strand=+, [457004:457163];C|synonymous_variant|LOW|CD630_03541|c.555A>C|p.Ile185Ile|555/567|185/188||WARNING_TRANSCRIPT_NO_START_CODON||WARNING_TRANSCRIPT_NO_START_CODON;C|intron_variant|MODIFIER|CD630_03540|c.30+561A>C||||CD630_03540|CD630_03540;T|synonymous_variant|LOW|CD630_03541|c.555A>T|p.Ile185Ile|555/567|185/188||WARNING_TRANSCRIPT_NO_START_CODON||WARNING_TRANSCRIPT_NO_START_CODON;"
yes outgroup:
"Non-coding SNP at 428665 > C,T functional=NULL_NULL_NULL locus_tag=CD630_03541 strand=+, [428257:428326];C|synonymous_variant|LOW|CD630_03541|c.555A>C|p.Ile185Ile|555/567|185/188||WARNING_TRANSCRIPT_NO_START_CODON||WARNING_TRANSCRIPT_NO_START_CODON;C|intron_variant|MODIFIER|CD630_03540|c.30+561A>C||||CD630_03540|CD630_03540;T|synonymous_variant|LOW|CD630_03541|c.555A>T|p.Ile185Ile|555/567|185/188||WARNING_TRANSCRIPT_NO_START_CODON||WARNING_TRANSCRIPT_NO_START_CODON;"

I didn't find this position in SNP matrix.

Similar to the previous issue, the yes_outgroup_matrix maps to two different loci, only one of which matches the locus_tag in the no-outgroup-matrix. This time, though, introns don't appear to play a part.
no outgroup
"Coding SNP at 473543 > C functional=NULL_NULL_NULL locus_tag=CD630_04010 strand=+;C|synonymous_variant|LOW|etfA1|c.87A>C|p.Ile29Ile|87/1038|29/345|etfA1|null or hypothetical protein;"
yes outgroup
"Non-coding SNP at 473543 > T,C functional=NULL_NULL_NULL locus_tag=CD630_04000 strand=+;C|synonymous_variant|LOW|CD630_04010|c.87A>C|p.Ile29Ile|87/1038|29/345|etfA1|etfA1;T|synonymous_variant|LOW|CD630_04010|c.87A>T|p.Ile29Ile|87/1038|29/345|etfA1|etfA1;"

Coding SNP at 473543 > T,C functional=NULL_NULL_NULL locus_tag=CD630_04010 Strand Information: CD630_04010=+;C|synonymous_variant|LOW|CD630_04010|c.87A>C|p.Ile29Ile|87/1038|29/345|etfA1|etfA1;T|synonymous_variant|LOW|CD630_04010|c.87A>T|p.Ile29Ile|87/1038|29/345|etfA1|etfA1;

The yes-outgroup variant has two locus tags (instead of just one) and has brackets whic are not found in no-outgroup variant.
no outgroup
"Coding SNP at 607587 > T functional=NULL_NULL_NULL locus_tag=CD630_05140 strand=+;T|synonymous_variant|LOW|cwpV|c.27A>T|p.Ala9Ala|27/4869|9/1622|cwpV|putative hemagglutinin/adhesin cwpV;"
yes outgroup
"Non-coding SNP at 607587 > C,T functional=NULL_NULL_NULL locus_tag=CD630_05130-CD630_05140 strand=+, [606702:606756]/+/;T|synonymous_variant|LOW|CD630_05140|c.27A>T|p.Ala9Ala|27/4869|9/1622|cwpV|cwpV;C|synonymous_variant|LOW|CD630_05140|c.27A>C|p.Ala9Ala|27/4869|9/1622|cwpV|cwpV;"

This is fixed. This position is supposed to have only one variant.
Coding SNP at 607587 > C functional=NULL_NULL_NULL locus_tag=CD630_05140 Strand Information: CD630_05140=+;C|synonymous_variant|LOW|cwpV|c.27A>C|p.Ala9Ala|27/4869|9/1622|cwpV|putative hemagglutinin/adhesin cwpV;

Locus tag is in many positions for no outgroup (is gene symbol and annotation missing? does it not exist?)
"Non-coding SNP at 747059 > A,T functional=NULL_NULL_NULL locus_tag=CD630_06250-CD630_06260 strand=+/+/;A|intergenic_region|MODIFIER|CD630_06250-CD630_06260|n.747059G>A||||CD630_06250-CD630_06260|CD630_06250-CD630_06260;T|intergenic_region|MODIFIER|CD630_06250-CD630_06260|n.747059G>T||||CD630_06250-CD630_06260|CD630_06250-CD630_06260;"

Considering this position doesn't have an annotation associated with it, snpeff prints out locus Ids. No bugs here:
Non-Coding SNP at 747059 > T,A functional=NULL_NULL_NULL locus_tag=CD630_06250-CD630_06260 Strand Information: CD630_06250=+/CD630_06260=+/;A|intergenic_region|MODIFIER|CD630_06250-CD630_06260|n.747059G>A||||CD630_06250-CD630_06260|CD630_06250-CD630_06260;T|intergenic_region|MODIFIER|CD630_06250-CD630_06260|n.747059G>T||||CD630_06250-CD630_06260|CD630_06250-CD630_06260;

1. When these is present in the row annotation --  ERROR_OUT_OF_CHROMOSOME_RANGE or locus_tag to CHR_END --
   change annotation to make the variant intergenic between the first and last gene of the chromosome.

Non-coding SNP at 4293521 > T,C,G functional=NULL_NULL_NULL locus_tag= strand=Null;
G||MODIFIER|||||||ERROR_OUT_OF_CHROMOSOME_RANGE||ERROR_OUT_OF_CHROMOSOME_RANGE;T||
MODIFIER|||||||ERROR_OUT_OF_CHROMOSOME_RANGE||ERROR_OUT_OF_CHROMOSOME_RANGE;C||MODIFIER
|||||||ERROR_OUT_OF_CHROMOSOME_RANGE||ERROR_OUT_OF_CHROMOSOME_RANGE;
Non-coding SNP at 4290130 > C functional=NULL_NULL_NULL locus_tag=CD630_36800 strand=-;
C|intergenic_region|MODIFIER|rpmH-CHR_END|n.4290130A>C||||rpmH|null or hypothetical protein;
1. Need strand information if a position is in two genes (that is, overlapping genes) because the genes
   could be on different strand

Non-coding SNP at 455792 > A,C functional=NULL_NULL_NULL locus_tag=CD630_03860 strand=-;A|
intron_variant|MODIFIER|CD630_03540|c.31-1213T>A||||CD630_03540|CD630_03540;C|
intron_variant|MODIFIER|CD630_03540|c.31-1213T>C||||CD630_03540|CD630_03540;C|synonymous_variant|
LOW|CD630_03860|c.819A>G|p.Val273Val|819/3045|273/1014|CD630_03860|CD630_03860;”
1. If one variant is in a non-coding region (intergenic, intron) and the other is in a coding region, we want
   to know that information. For example: mutation in CD630_03860 is coding, but it says non-coding because of
   the intron variant

Non-coding SNP at 455792 > A,C functional=NULL_NULL_NULL locus_tag=CD630_03860 strand=-;A|
intron_variant|MODIFIER|CD630_03540|c.31-1213T>A||||CD630_03540|CD630_03540;C|
intron_variant|MODIFIER|CD630_03540|c.31-1213T>C||||CD630_03540|CD630_03540;C|synonymous_variant|
LOW|CD630_03860|c.819A>G|p.Val273Val|819/3045|273/1014|CD630_03860|CD630_03860;”
1. There is some bug producing brackets contained ###:### after the strand information in certain row annotations
   Coding SNP at 2093672 > G functional=NULL_NULL_NULL locus_tag=CD630_18090 strand=+,
   [2092758:2093730];G|missense_variant|MODERATE|CD630_18090|c.1112T>G|p.Met371Arg|1112/1170|371/389|
   null or hypothetical protein|Fragment of putative permease, MFS family;

Partially fixed. Need to add "intergenic region" in the annotations.

No protein_coding/intergenic_region field in ANN at 4293521 > T,C,G functional=NULL_NULL_NULL locus_tag=NULL Strand Information: NULL=No Strand Information found;G||MODIFIER|||||||rpmH-dnaA||rpmH-dnaA;T||MODIFIER|||||||rpmH-dnaA||rpmH-dnaA;C||MODIFIER|||||||rpmH-dnaA||rpmH-dnaA;

This is fixed. Now both the locus tags has separate strand information.

Coding SNP at 455792 > A,C functional=NULL_NULL_NULL locus_tag=CD630_03540-CD630_03860 Strand Information: CD630_03540=+/CD630_03860=-/;A|intron_variant|MODIFIER|CD630_03540|c.31-1213T>A||||CD630_03540|CD630_03540;C|intron_variant|MODIFIER|CD630_03540|c.31-1213T>C||||CD630_03540|CD630_03540;C|synonymous_variant|LOW|CD630_03860|c.819A>G|p.Val273Val|819/3045|273/1014|CD630_03860|CD630_03860;

I spoke to stephanie about this and we will be considering intron variant as coding.

Coding SNP at 455792 > A,C functional=NULL_NULL_NULL locus_tag=CD630_03540-CD630_03860 Strand Information: CD630_03540=+/CD630_03860=-/;A|intron_variant|MODIFIER|CD630_03540|c.31-1213T>A||||CD630_03540|CD630_03540;C|intron_variant|MODIFIER|CD630_03540|c.31-1213T>C||||CD630_03540|CD630_03540;C|synonymous_variant|LOW|CD630_03860|c.819A>G|p.Val273Val|819/3045|273/1014|CD630_03860|CD630_03860;

This is fixed.

Coding SNP at 2093672 > G functional=NULL_NULL_NULL locus_tag=CD630_18090 Strand Information: CD630_18090=+;G|missense_variant|MODERATE|CD630_18090|c.1112T>G|p.Met371Arg|1112/1170|371/389|null or hypothetical protein|Fragment of putative permease, MFS family;

In the current test matrix, "/scratch/esnitkin_fluxod/apirani/Project_Cdiff/Analysis/Project_propensity_score_match/2019_05_14_PSM_variant_calling/core_temp_dir/test_data/SNP_matrix_allele_new.csv" there are multiple issues with the file and now I can't open it. Several rows, including 35438, do not have the expected number of elements when I tried to read them into R using the following code:    read.table("/scratch/esnitkin_fluxod/apirani/Project_Cdiff/Analysis/Project_propensity_score_match/2019_05_14_PSM_variant_calling/core_temp_dir/test_data/SNP_matrix_allele_new.csv",
header = TRUE,
stringsAsFactors = FALSE,
sep = "\t",
quote = "",
row.names = 1)
Any ideas why this might be happening?

WARNING_TRANSCRIPT_NO_START_CODON still in some row names for mutli-allelic sites. Do you know what snpeff is trying to say with this warning message? How should we handle these moving forward?

These following SNPs are non-coding but intragenic. What does this mean-- are they before a start codon or after a stop codon? What are the CD630_r00#0 genes? Did you create these to resolve a bug?
[1] "Non-Coding SNP at 15966 > A functional=NULL_NULL_NULL locus_tag=CD630_r0030 Strand Information: CD630_r0030=+;A|intragenic_variant|MODIFIER|5s_rRNA|n.15966G>A||||5s rRNA|5S ribosomal RNA;"
[2] "Non-Coding SNP at 129207 > A functional=NULL_NULL_NULL locus_tag=CD630_r0090 Strand Information: CD630_r0090=+;A|intragenic_variant|MODIFIER|5s_rRNA|n.129207G>A||||5s rRNA|5S ribosomal RNA;"
[3] "Non-Coding SNP at 129225 > C functional=NULL_NULL_NULL locus_tag=CD630_r0090 Strand Information: CD630_r0090=+;C|intragenic_variant|MODIFIER|5s_rRNA|n.129225T>C||||5s rRNA|5S ribosomal RNA;"
[4] "Non-Coding SNP at 129282 > A functional=NULL_NULL_NULL locus_tag=CD630_r0090 Strand Information: CD630_r0090=+;A|intragenic_variant|MODIFIER|5s_rRNA|n.129282G>A||||5s rRNA|5S ribosomal RNA;"
[5] "Non-Coding SNP at 152191 > A functional=NULL_NULL_NULL locus_tag=CD630_r0180 Strand Information: CD630_r0180=+;A|intragenic_variant|MODIFIER|5s_rRNA|n.152191C>A||||5s rRNA|5S ribosomal RNA;"
[6] "Non-Coding SNP at 382210 > G functional=NULL_NULL_NULL locus_tag=CD630_r0210 Strand Information: CD630_r0210=+;G|intragenic_variant|MODIFIER|5s_rRNA|n.382210A>G||||5s rRNA|5S ribosomal RNA;"

In the current test matrix, "/scratch/esnitkin_fluxod/apirani/Project_Cdiff/Analysis/Project_propensity_score_match/2019_05_14_PSM_variant_calling/core_temp_dir/test_data/SNP_matrix_allele_new.csv" there are multiple issues with the file and now I can't open it. Several rows, including 35438, do not have the expected number of elements when I tried to read them into R using the following code: read.table("/scratch/esnitkin_fluxod/apirani/Project_Cdiff/Analysis/Project_propensity_score_match/2019_05_14_PSM_variant_calling/core_temp_dir/test_data/SNP_matrix_allele_new.csv",
header = TRUE,
stringsAsFactors = FALSE,
sep = "\t",
quote = "",
row.names = 1)
Any ideas why this might be happening?

WARNING_TRANSCRIPT_NO_START_CODON still in some row names for mutli-allelic sites. Do you know what snpeff is trying to say with this warning message? How should we handle these moving forward?

snpeff defines it as: A protein coding transcript does not have a proper START codon. It is rare that a real transcript does not have a START codon, so this probably indicates an error or missing information in the reference genome.
want to check the genes where this might be happening? I probably think its an annotation file issue.

In the current test matrix, "/scratch/esnitkin_fluxod/apirani/Project_Cdiff/Analysis/Project_propensity_score_match/2019_05_14_PSM_variant_calling/core_temp_dir/test_data/SNP_matrix_allele_new.csv" there are multiple issues with the file and now I can't open it. Several rows, including 35438, do not have the expected number of elements when I tried to read them into R using the following code: read.table("/scratch/esnitkin_fluxod/apirani/Project_Cdiff/Analysis/Project_propensity_score_match/2019_05_14_PSM_variant_calling/core_temp_dir/test_data/SNP_matrix_allele_new.csv",
header = TRUE,
stringsAsFactors = FALSE,
sep = "\t",
quote = "",
row.names = 1)
Any ideas why this might be happening?

This issue is occurs only for positions that fall under functional class filters such as functional=NULL_REPEATS_NULL

In the current test matrix, "/scratch/esnitkin_fluxod/apirani/Project_Cdiff/Analysis/Project_propensity_score_match/2019_05_14_PSM_variant_calling/core_temp_dir/test_data/SNP_matrix_allele_new.csv" there are multiple issues with the file and now I can't open it. Several rows, including 35438, do not have the expected number of elements when I tried to read them into R using the following code: read.table("/scratch/esnitkin_fluxod/apirani/Project_Cdiff/Analysis/Project_propensity_score_match/2019_05_14_PSM_variant_calling/core_temp_dir/test_data/SNP_matrix_allele_new.csv",
header = TRUE,
stringsAsFactors = FALSE,
sep = "\t",
quote = "",
row.names = 1)
Any ideas why this might be happening?

This issue is fixed now.

Awesome, Ali! Thank you!
When it’s made can you let me know when you have this newest/fixed version of the SNP matrix? I want to update the variant parser based on this version so that I can use this updated matrix for my ASM presentation.
-Katie

On Jun 11, 2019, at 9:58 AM, Ali Pirani<EMAIL_ADDRESS>wrote:
External Email - Use Caution
In the current test matrix, "/scratch/esnitkin_fluxod/apirani/Project_Cdiff/Analysis/Project_propensity_score_match/2019_05_14_PSM_variant_calling/core_temp_dir/test_data/SNP_matrix_allele_new.csv" there are multiple issues with the file and now I can't open it. Several rows, including 35438, do not have the expected number of elements when I tried to read them into R using the following code: read.table("/scratch/esnitkin_fluxod/apirani/Project_Cdiff/Analysis/Project_propensity_score_match/2019_05_14_PSM_variant_calling/core_temp_dir/test_data/SNP_matrix_allele_new.csv",
header = TRUE,
stringsAsFactors = FALSE,
sep = "\t",
quote = "",
row.names = 1)
Any ideas why this might be happening?
This issue is fixed now.
—
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One issue in the matrix is that the intergenic region Non-Coding SNPs near the locus CD630_36800 have only 1 gene in the locus_tag (CD630_36800) but the SNP is between two genes rpmH and dnaA. I think this is the last gene in the genome (maybe?) so you may need to handle this special case.
1] "Non-Coding SNP at 4289619 > C functional=NULL_NULL_NULL locus_tag=CD630_36800 Strand Information: CD630_36800=-;C|intergenic_region|MODIFIER|rpmH-dnaA|n.4289619T>C||||rpmH|null or hypothetical protein;"
[2] "Non-Coding SNP at 4289692 > C functional=NULL_NULL_NULL locus_tag=CD630_36800 Strand Information: CD630_36800=-;C|intergenic_region|MODIFIER|rpmH-dnaA|n.4289692T>C||||rpmH|null or hypothetical protein;"
[3] "Non-Coding SNP at 4289722 > C functional=NULL_NULL_NULL locus_tag=CD630_36800 Strand Information: CD630_36800=-;C|intergenic_region|MODIFIER|rpmH-dnaA|n.4289722A>C||||rpmH|null or hypothetical protein;"
[4] "Non-Coding SNP at 4289777 > T functional=NULL_NULL_NULL locus_tag=CD630_36800 Strand Information: CD630_36800=-;T|intergenic_region|MODIFIER|rpmH-dnaA|n.4289777C>T||||rpmH|null or hypothetical protein;"
[5] "Non-Coding SNP at 4289989 > A functional=NULL_NULL_NULL locus_tag=CD630_36800 Strand Information: CD630_36800=-;A|intergenic_region|MODIFIER|rpmH-dnaA|n.4289989C>A||||rpmH|null or hypothetical protein;"
[6] "Non-Coding SNP at 4290189 > G functional=NULL_NULL_NULL locus_tag=CD630_36800 Strand Information: CD630_36800=-;G|intergenic_region|MODIFIER|rpmH-dnaA|n.4290189A>G||||rpmH|null or hypothetical protein;"

One issue in the matrix is that the intergenic region Non-Coding SNPs near the locus CD630_36800 have only 1 gene in the locus_tag (CD630_36800) but the SNP is between two genes rpmH and dnaA. I think this is the last gene in the genome (maybe?) so you may need to handle this special case.
1] "Non-Coding SNP at 4289619 > C functional=NULL_NULL_NULL locus_tag=CD630_36800 Strand Information: CD630_36800=-;C|intergenic_region|MODIFIER|rpmH-dnaA|n.4289619T>C||||rpmH|null or hypothetical protein;"
[2] "Non-Coding SNP at 4289692 > C functional=NULL_NULL_NULL locus_tag=CD630_36800 Strand Information: CD630_36800=-;C|intergenic_region|MODIFIER|rpmH-dnaA|n.4289692T>C||||rpmH|null or hypothetical protein;"
[3] "Non-Coding SNP at 4289722 > C functional=NULL_NULL_NULL locus_tag=CD630_36800 Strand Information: CD630_36800=-;C|intergenic_region|MODIFIER|rpmH-dnaA|n.4289722A>C||||rpmH|null or hypothetical protein;"
[4] "Non-Coding SNP at 4289777 > T functional=NULL_NULL_NULL locus_tag=CD630_36800 Strand Information: CD630_36800=-;T|intergenic_region|MODIFIER|rpmH-dnaA|n.4289777C>T||||rpmH|null or hypothetical protein;"
[5] "Non-Coding SNP at 4289989 > A functional=NULL_NULL_NULL locus_tag=CD630_36800 Strand Information: CD630_36800=-;A|intergenic_region|MODIFIER|rpmH-dnaA|n.4289989C>A||||rpmH|null or hypothetical protein;"
[6] "Non-Coding SNP at 4290189 > G functional=NULL_NULL_NULL locus_tag=CD630_36800 Strand Information: CD630_36800=-;G|intergenic_region|MODIFIER|rpmH-dnaA|n.4290189A>G||||rpmH|null or hypothetical protein;"

Yes, since its at the end of the chromosome, we are substituting rpmH-CHR_END with rpmH-dnaA where dnaA is the first gene in chromosome.

The number of delimiters (in this case, pipes) is not a multiple of 9 for certain annotations (see below, number of pipes on top and counts on bottom)
0      9          18         22      27     29     31   33  36
6 279830  10035    512    125      1      3      7      2
this happens when there are warnings:
WARNING_TRANSCRIPT_NO_START_CODON
WARNING_TRANSCRIPT_MULTIPLE_STOP_CODONS

Some of the genes in my matrix (ex: CD630_00040) have variants with the WARNING_TRANSCRIPT_NO_START_CODON, but other variants (same gene) have normal annotations. what is causing this problem? Actually, I looked at a specific variant in this gene, Asn352Asp, and found that it has the "WARNING_TRANSCRIPT_NO_START" error in the two VCF files in the snpeff output but that is not included in the snpmat row name. Same with other variants in this gene so I don't think SNPeff is being inconsistent -- (it's wrong, for sure, but not inconsistent).

incorrect number of pipes - seems to be in the replacement for the "end" of the chromosome  (CHR_END)
No protein_coding/intergenic_region field in ANN at 4290731 > A,T functional=NULL_NULL_NULL locus_tag=NULL Strand Information: NULL=No Strand Information found;A||MODIFIER|||||||rpmH-dnaA||rpmH-dnaA;T||MODIFIER|||||||rpmH-dnaA||rpmH-dnaA;”

CHR_END is still present in the row annotations, but should be instead the first gene in the reference genome
[3] "Non-Coding SNP at 4289975 > A,T functional=NULL_NULL_NULL locus_tag=CD630_36800-CHR_END Strand Information: CD630_36800=-/CHR_END=No Strand Information found/;T|intergenic_region|MODIFIER|CD630_36800-dnaA|n.4289975G>T||||rpmH-dnaA|rpmH-dnaA"

Coding SNP at 2213121 > A,C functional=NULL_NULL_NULL locus_tag=CD630_19120-CD630_19270 Strand Information: CD630_19120=+/CD630_19270=-/;A|missense_variant|MODERATE|CD630_19120|c.207T>A|p.Asp69Glu|207/1434|69/477|eutA|eutA;C|synonymous_variant|LOW|CD630_19120|c.207T>C|p.Asp69Asp|207/1434|69/477|eutA|eutA;A|intron_variant|MODIFIER|CD630_19270|c.595-6938A>T||||CD630_19270|CD630_19270;
This is a multiallelic site: T->A, C. It also is a position that is in two genes. Thus, there should be 4 annotations, not 3. Annotations for T->A, T->C (both positive strand), and A->T and A->G (the complement on the negative strand).
Why is there no annotation for A -> G?

Change pipe-delimited field 4 to ALWAYS be locus tag, and NEVER gene symbol. Currently, the gene symbol is reported if there is a gene symbol, else the locus tag is reported.
Particularly when lines with multiple annotations are split on to separate row, this makes it impossible to cross reference the gene symbol to the strand information. In this case, I don't know what gene symbol sig K is.
"Coding SNP at 1431118 > C functional=NULL_NULL_NULL locus_tag=CD630_12310-CD630_12300 Strand Information: CD630_12310=-/CD630_12300=-/;C|missense_variant|MODERATE|CD630_12310|c.119A>G|p.Asn40Ser|119/1518|40/505|null or hypothetical protein,sigK|putative site-specific recombinase,Sigma K,;C|intron_variant|MODIFIER|sigK|c.391-1437A>G||||null or hypothetical protein,sigK|putative site-specific recombinase,Sigma K,;"

This is a SNV in the intergenic region between rpmH and dnaA. Only one locus tag is reported and correspondingly only one strand. Should be reporting the locus tag and strand info for both rpmH and dnaA. Also, is this only reporting annotation for rpmH ad not dnaA?
"Non-Coding SNP at 4289777 > T functional=NULL_NULL_NULL locus_tag=CD630_36800 Strand Information: CD630_36800=-;T|intergenic_region|MODIFIER|rpmH-dnaA|n.4289777C>T||||rpmH|null or hypothetical protein;"
"Non-Coding SNP at 4289861 > T functional=NULL_NULL_NULL locus_tag=CD630_36800 Strand Information: CD630_36800=-;T|intergenic_region|MODIFIER|rpmH-dnaA|n.4289861C>T||||rpmH|null or hypothetical protein;"

When there are multiallelic sites in the intergenic region between the last and beginning of the genome, the annotation looks different than if there is one allele:
BI-ALLELIC
"Non-Coding SNP at 4289777 > T functional=NULL_NULL_NULL locus_tag=CD630_36800 Strand Information: CD630_36800=-;T|intergenic_region|MODIFIER|rpmH-dnaA|n.4289777C>T||||rpmH|null or hypothetical protein;"
MULTI-ALLELIC
"No protein_coding/intergenic_region field in ANN at 4290800 > A,T functional=NULL_NULL_NULL locus_tag=NULL Strand Information: NULL=No Strand Information found;A||MODIFIER|||||||rpmH-dnaA||rpmH-dnaA;T||MODIFIER|||||||rpmH-dnaA||rpmH-dnaA;"

When a SNV is present in multiple genes (in this case 3 genes), only 2 locus tags/strand info are listed and not 3 -- here: CD630_18440, CD630_18560, CD630_18550
Coding SNP at 2145246 > G functional=NULL_NULL_NULL locus_tag=CD630_18550-CD630_18440 Strand Information: CD630_18550=+/CD630_18440=+/;G|missense_variant|MODERATE|CD630_18550|c.308A>G|p.Gln103Arg|308/390|103/129|null or hypothetical protein,null or hypothetical protein|null or hypothetical protein,conserved repeat protein,;G|intron_variant|MODIFIER|CD630_18440|c.1233+7785A>G||||null or hypothetical protein,null or hypothetical protein|null or hypothetical protein,conserved repeat protein,;G|missense_variant|MODERATE|CD630_18560|c.7A>G|p.Lys3Glu|7/2430|3/809|null or hypothetical protein,null or hypothetical protein|null or hypothetical protein,conserved repeat protein,;

Similar to the CHR_END issue, sometimes the annotation will say CHR_START - GENE. Change to CHR_START to the last gene in the genome?
"Non-Coding SNP at 265 > T functional=NULL_NULL_NULL locus_tag=KPNIH1_00005 Strand Information: KPNIH1_00005=-;T|intergenic_region|MODIFIER|CHR_START-KPNIH1_00005|n.265C>T||||null or hypothetical protein|FMN-binding protein MioC;"

Coding SNP at 2213121 > A,C functional=NULL_NULL_NULL locus_tag=CD630_19120-CD630_19270 Strand Information: CD630_19120=+/CD630_19270=-/;A|missense_variant|MODERATE|CD630_19120|c.207T>A|p.Asp69Glu|207/1434|69/477|eutA|eutA;C|synonymous_variant|LOW|CD630_19120|c.207T>C|p.Asp69Asp|207/1434|69/477|eutA|eutA;A|intron_variant|MODIFIER|CD630_19270|c.595-6938A>T||||CD630_19270|CD630_19270;
This is a multiallelic site: T->A, C. It also is a position that is in two genes. Thus, there should be 4 annotations, not 3. Annotations for T->A, T->C (both positive strand), and A->T and A->G (the complement on the negative strand).
Why is there no annotation for A -> G?

Check this positions in IGV.

sigK

Change pipe-delimited field 4 to ALWAYS be locus tag, and NEVER gene symbol. Currently, the gene symbol is reported if there is a gene symbol, else the locus tag is reported.
Particularly when lines with multiple annotations are split on to separate row, this makes it impossible to cross reference the gene symbol to the strand information. In this case, I don't know what gene symbol sig K is.
"Coding SNP at 1431118 > C functional=NULL_NULL_NULL locus_tag=CD630_12310-CD630_12300 Strand Information: CD630_12310=-/CD630_12300=-/;C|missense_variant|MODERATE|CD630_12310|c.119A>G|p.Asn40Ser|119/1518|40/505|null or hypothetical protein,sigK|putative site-specific recombinase,Sigma K,;C|intron_variant|MODIFIER|sigK|c.391-1437A>G||||null or hypothetical protein,sigK|putative site-specific recombinase,Sigma K,;"
Also, sometimes the annotation is in pipe-delimited field 4 instead of locus tag or gene symbol
"Non-Coding SNP at 5393980 > T functional=NULL_NULL_NULL locus_tag=KPNIH1_26385 Strand Information: KPNIH1_26385=-;T|intergenic_region|MODIFIER|KPNIH1_26385-null or hypothetical protein|n.5393980A>T||||null or hypothetical protein|hypothetical protein;"

Remove gene symbol and insert Locus Tag.

Change pipe-delimited field 4 to ALWAYS be locus tag, and NEVER gene symbol. Currently, the gene symbol is reported if there is a gene symbol, else the locus tag is reported.
Particularly when lines with multiple annotations are split on to separate row, this makes it impossible to cross reference the gene symbol to the strand information. In this case, I don't know what gene symbol sig K is.
"Coding SNP at 1431118 > C functional=NULL_NULL_NULL locus_tag=CD630_12310-CD630_12300 Strand Information: CD630_12310=-/CD630_12300=-/;C|missense_variant|MODERATE|CD630_12310|c.119A>G|p.Asn40Ser|119/1518|40/505|null or hypothetical protein,sigK|putative site-specific recombinase,Sigma K,;C|intron_variant|MODIFIER|sigK|c.391-1437A>G||||null or hypothetical protein,sigK|putative site-specific recombinase,Sigma K,;"
Also, sometimes the annotation is in pipe-delimited field 4 instead of locus tag or gene symbol
"Non-Coding SNP at 5393980 > T functional=NULL_NULL_NULL locus_tag=KPNIH1_26385 Strand Information: KPNIH1_26385=-;T|intergenic_region|MODIFIER|KPNIH1_26385-null or hypothetical protein|n.5393980A>T||||null or hypothetical protein|hypothetical protein;"

Duplicate issue - resolved
Remove gene symbol and insert Locus Tag in field 4 #30

sigK

Change pipe-delimited field 4 to ALWAYS be locus tag, and NEVER gene symbol. Currently, the gene symbol is reported if there is a gene symbol, else the locus tag is reported.
Particularly when lines with multiple annotations are split on to separate row, this makes it impossible to cross reference the gene symbol to the strand information. In this case, I don't know what gene symbol sig K is.
"Coding SNP at 1431118 > C functional=NULL_NULL_NULL locus_tag=CD630_12310-CD630_12300 Strand Information: CD630_12310=-/CD630_12300=-/;C|missense_variant|MODERATE|CD630_12310|c.119A>G|p.Asn40Ser|119/1518|40/505|null or hypothetical protein,sigK|putative site-specific recombinase,Sigma K,;C|intron_variant|MODIFIER|sigK|c.391-1437A>G||||null or hypothetical protein,sigK|putative site-specific recombinase,Sigma K,;"
Also, sometimes the annotation is in pipe-delimited field 4 instead of locus tag or gene symbol
"Non-Coding SNP at 5393980 > T functional=NULL_NULL_NULL locus_tag=KPNIH1_26385 Strand Information: KPNIH1_26385=-;T|intergenic_region|MODIFIER|KPNIH1_26385-null or hypothetical protein|n.5393980A>T||||null or hypothetical protein|hypothetical protein;"

Remove gene symbol and insert Locus Tag.

Duplicate issue - resolved
Remove gene symbol and insert Locus Tag in field 4 #30

When a SNV is present in multiple genes (in this case 3 genes), only 2 locus tags/strand info are listed and not 3 -- here: CD630_18440, CD630_18560, CD630_18550
Coding SNP at 2145246 > G functional=NULL_NULL_NULL locus_tag=CD630_18550-CD630_18440 Strand Information: CD630_18550=+/CD630_18440=+/;G|missense_variant|MODERATE|CD630_18550|c.308A>G|p.Gln103Arg|308/390|103/129|null or hypothetical protein,null or hypothetical protein|null or hypothetical protein,conserved repeat protein,;G|intron_variant|MODIFIER|CD630_18440|c.1233+7785A>G||||null or hypothetical protein,null or hypothetical protein|null or hypothetical protein,conserved repeat protein,;G|missense_variant|MODERATE|CD630_18560|c.7A>G|p.Lys3Glu|7/2430|3/809|null or hypothetical protein,null or hypothetical protein|null or hypothetical protein,conserved repeat protein,;

Resolved


Bank Account: fix links in instructions

In the Bank Account exercise, the [instructions.append.md] has some links that could use some formatting:

Tasks

Put these links in a list. The text for the links should be descriptive of the link, by including the source of the link and its title. For instance, a good text for https://tour.golang.org/concurrency/9 would be Tour Of Go: sync.Mutex. For list and link formatting in markdown, check Markdown Exercism's Style Guide.

Contributing to this issue

If you'd like to contribute to this issue, just make a comment below saying that you'd like to work on this. After that, feel free to open a PR with the fix and link it to this issue. See more information on how to link PRs to issues on Linking a pull request to an issue.
If you have further questions on how to solve this issue or get stuck in the middle of solving it, post your concerns/questions below and we'll help you!

@andrerfcsantos just noticed. would like to contribute this if you don't mind. :)

@Jasstkn Go for it :)


[Power Support] Update build configuration files to support IBM Power platform (for ruby and libpq packages)

This PR is made to provide IBM Power support to BOSH.
You can find details of the issue in this PR https://github.com/cloudfoundry/bosh/pull/892. I've come to the idea of this changes thanking to Matthew Sykes (and his post in cf-dev).

Hey @allomov. We typically want to avoid usage of pre_packaging scripts (since they run in a deterministic environment) and requiring internet access. For this PR it should be really simple to resolve it. Just commit files being downloaded into the src directory and then replace config files in the appropriate packaging scripts if ppc64le.

@cppforlife I fully agree with you about using pre_packaging scripts. I used pre_packaging script to  show you the source of config.guess file. Also I was not sure about where to place config.guess file. Is it ok to place it to src/common/config.guess?

I would just create src/config/config.guess and src/config/config.sub.

Ok. Thank you for advise.


copy (with attribution) scraper.py for gcp instance cost scraping

Copied scraper.py from MIT-licensed repo: https://github.com/doitintl/gcpinstances.info

Confirmed with Gavin Zee that this is appropriate for incorporating MIT-licensed code.


Fix typos in Validated

I edited mainly to correct a few uncontroversial typos—"cause" where "case" is intended, a missing closing brace in a code sample, etc.—but also included a few other minor things here that I felt read better.
Hyphens are changed to em dashes where appropriate, which isn't obvious in a monospace diff.

LGTM, thanks for your contribution


addresses typos, syntax and rewordings after reading through tutorial

PR Checklist

[x] A description of the changes is added to the description of this PR.
[ ] If there is a related issue, make sure it is linked to this PR.
[ ] If you've fixed a bug or added code that should be tested, add tests!
[ ] If you've added or modified a feature, documentation in docs is updated

Description of changes
This PR introduces typos fixes, edits, Markdown syntax changes, and rewordings based on my understanding of the Tutorial document. I tried to only make chances that enhanced the document without altering the original voice of the author(s).

Thank you to the creators and contributors for open sourcing Unity Catalog! I'm excited to see how my team and I will be able to incorporate it into our work!

@tdas, happy to help! I'm really excited by UC, so I'm grateful for all the stellar work your team is doing in this area.
I left a clarifying comment and a question, so once you respond, I will make the necessary changes.

@tdas, ready for re-review at your convenience.


ZER-185 Change text in drop down lists in data input block

dev
JIRA

ZER-185

Code reviewers

[ ] @loqimean

Summary of issue
As a user, I want to see numbers with words in drop-down lists so that the choice will be easier for understanding.
Acceptance criteria:
GIVEN the user wants to choose the child’s age on the calculator page
WHEN he/she is clicking on ‘years’ and ‘months’
THEN ‘0 years; 1 year; 2 years’ is displayed for ‘years’
AND ‘1 month; 0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 months’ is displayed for ‘months’
See the exact texts in the file: https://docs.google.com/document/d/1ezwQR3gtY06rKcotLiFJE_XJBqnw5I1RuzTHiywW4eU/edit
English:

Ukrainian:

Summary of change
English:
Added words 'year' and 'years' for the corresponding values in years dropdown. Similar for months dropdown

Ukrainian:
Added words 'років', 'рік', 'роки' for the corresponding values in years dropdown. Similar for months dropdown

Additional changes:
Set attribute 'hidden' for values above '0 years' or '0 months' values
Testing approach
ToDo
CHECK LIST

[x]  СI passed
[x]  Сode coverage >=95%
[x]  PR is reviewed manually again (to make sure you have 100% ready code)
[x]  All reviewers agreed to merge the PR
[x]  I've checked new feature as logged in and logged out user if needed
[x]  PR meets all conventions

https://stackoverflow.com/questions/6166064/i18n-pluralization

таким чином пробував?

таким чином пробував?

Та, можеш глянути перші коміти. А так, то рішили з Іваном піти цікавішим шляхом)


From private repo

@ShannonLeavitt : Thanks for your contribution! The author(s) have been notified to review your proposed change.


quick patch that lets someone with write access restart a build

Thanks for this @bradrydzewski, this has been niggling me for some time.
It seems like I'm still seeing an issue where the rebuild button is not visible for users that have write access to the repo but are not repo admins. Looking at the angular conditions, it seems like the button needs repo.role to be populated because it checks repo.role.admin and repo.role.write. Looking at the json response from handler.GetRepo ("/api/repos/:host/:owner/:name") for one of the users that isn't seeing the button, it turns out there is no repo.role object. Seem like it just totally skips it at the if role.Admin == false { line in handler/repo.go (around line 32).
Is the solution to simply include the role object, but exclude the public_key & params? Something like:
if role.Admin == false {
	json.NewEncoder(w).Encode(struct {
		*model.Repo
		Perm      *model.Perm `json:"role"`
	}{repo, role})
	return
}

I'm happy to make the change and submit a PR but just wanted to make sure this this would work and wasn't going to cause other issues.


Must have struct for json to work, not nil

Description

Fixes a bug in the new github package to properly handle the json unmarshal. It turns out using a nil uninitialized pointer is not supported (leads to the following runtime error):
Error loading configured Github App Config JSON: json: Unmarshal(nil *github.GithubAppConfig)

TODOs
Please ensure all of these TODOs are completed before asking for a review.

[x] Ensure the branch is named correctly with the issue number. e.g: feature/new-vpc-endpoints-955 or bug/missing-count-param-434.
[x] Update the docs.
[x] Keep the changes backward compatible where possible.
[x] Run the pre-commit checks successfully.
[x] Run the relevant tests successfully.
[x] Ensure any 3rd party code adheres with our license policy or delete this line if its not applicable.

Thanks for review! Merging now.


Issue/4296 hardcoded strings (#4363)

Pull request opened by the merge tool on behalf of #4363

Merged in 28091ef9b750a62c5c135574cefe37557ccf0e59


Adding operationCount metric in preparation to replace operationRate

In order to record more accurate and time-wise precise request rates we're going to test using Count metric as opposed to Meter (which is an average of 1, 5 and 15 minute periods)

Codecov Report

Merging #1336 into master will increase coverage by <.01%.
The diff coverage is 100%.

@@             Coverage Diff              @@
##             master    #1336      +/-   ##
============================================
+ Coverage     72.16%   72.16%   +<.01%
  Complexity     6513     6513
============================================
  Files           473      473
  Lines         37272    37274       +2
  Branches       4713     4713
============================================
+ Hits          26897    26899       +2
  Misses         9113     9113
  Partials       1262     1262

Impacted Files
Coverage Δ
Complexity Δ

...java/com.github.ambry/rest/RestRequestMetrics.java
100% <100%> (ø)
4 <0> (ø)
:arrow_down:

...m.github.ambry/rest/RestRequestMetricsTracker.java
96.34% <100%> (+0.04%)
15 <0> (ø)
:arrow_down:

.../com.github.ambry.network/BlockingChannelInfo.java
76.98% <0%> (-3.97%)
15% <0%> (-1%)

...c/main/java/com.github.ambry.network/Selector.java
78.21% <0%> (-1.84%)
77% <0%> (-2%)

...java/com.github.ambry.network/SSLTransmission.java
71.38% <0%> (-0.62%)
76% <0%> (-1%)

...va/com.github.ambry.rest/NettyResponseChannel.java
91.82% <0%> (-0.22%)
117% <0%> (-1%)

...in/java/com.github.ambry.store/BlobStoreStats.java
70.83% <0%> (-0.21%)
103% <0%> (ø)

...rc/main/java/com.github.ambry.store/BlobStore.java
89.54% <0%> (ø)
99% <0%> (ø)
:arrow_down:

...ls/src/main/java/com.github.ambry.utils/Utils.java
76.89% <0%> (+0.33%)
114% <0%> (+1%)
:arrow_up:

...src/main/java/com.github.ambry.commons/BlobId.java
93.4% <0%> (+0.34%)
74% <0%> (+1%)
:arrow_up:

... and 4 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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⚠ Bofrost.fr has degraded performance

In 9209f05, Bofrost.fr (https://www.bofrost.fr) experienced degraded performance:

HTTP code: 200
Response time: 950 ms

Resolved: Bofrost.fr performance has improved in e493fec after 6 minutes.


Support shared LoadBalancerIP for multiple Services

Users want to share LoadBalancerIP between multiple Services when they face external IP shortage. It's possible to do it when the Services sharing an IP meet the requirements:

The Services use different ports
The Services use the Cluster external traffic policy, or they have identical Endpoints.

However, the ability of using any IP that is already allocated to another Service may incur a security risk that a Service can "steal" LoadBalancer traffic intended for another Service.
To support the use case without introducing the security risk, we use the annotation service.antrea.io/allow-shared-load-balancer-ip: true on Services to restrict IPs that can be shared. Services without the annotation will continue to have their LoadBalancerIPs exclusively used. Services with the annotation can share an IP between themselves when requesting the same IP.
Ideally, we should also check if the Services meet the first two requirements before assigning the IP to them. However, it's difficult to prevent Services from being changed to not meet the requirements after they get the IP assigned. Therefore, we assume that users using the feature know how to configure Services properly.
Fixes #4309

/test-all

Are you planning on adding an e2e test for the "normal" case in a follow-up PR?

I'm working e2e test, will add it to this PR.

More of a theoretical question for you: if the ServiceExternalIP feature was not itself Alpha, would you have introduced a feature gate for this? I know that the feature only becomes "active" if the annotation is used, but I remember you saying in the past that we were too liberal with introducing new functionality without a corresponding feature gate (e.g., FQDN support in Network Policies). I guess this may not apply here given that ServiceExternalIP is still Alpha and we can consider this an integral part of the ServiceExternalIP feature.

Yes, if ServiceExternalIP were enabled by default, I may add a new feature gate. I feel currently this doesn't require a new feature gate because of the same reason you think: this can be considered a part of the ServiceExternalIP feature, and the graduation of ServiceExternalIP feature gate will cover the capacity to share IPs.

/test-all


Generate DDL for whole table is missing column comments

System information:

OS: Linux Mint 20
DBeaver version: 21.0.2 EA, 21.0.0

Connection specification:

Database: Postgresql 12

Describe the problem you're observing:
The DDL function (DDL tab) in table detail for table with columns with comments doesn't create those comments.
Steps to reproduce
Use any table, for example
CREATE TABLE public.testtable (
	id serial NOT NULL,
	testchar varchar NULL,
	CONSTRAINT testtable_pkey PRIMARY KEY (id)
);
COMMENT ON COLUMN public.testtable.testchar IS 'this is my comment';

Try to get DDL for whole table. Use the tab DDL in the table.
The result SQL is:
CREATE TABLE public.testtable (
	id serial NOT NULL,
	testchar varchar NULL,
	CONSTRAINT testtable_pkey PRIMARY KEY (id)
);

When I use table list function Generate SQL - DDL, it works:
-- public.testtable definition

-- Drop table

-- DROP TABLE public.testtable;

CREATE TABLE public.testtable (
	id serial NOT NULL,
	testchar varchar NULL, -- this is my comment
	CONSTRAINT testtable_pkey PRIMARY KEY (id)
);

-- Column comments

COMMENT ON COLUMN public.testtable.testchar IS 'this is my comment';

hello @elring
Table and column comments are not default part of table DDL, so we added button "Show comments" in table tab "DDL" and in Generate->DDL

Are they working?

OK, my mistake. It works, I just didn't noticed the settings. I'm sorry :)


Upgrade Retrofit up to 2.+ version

https://speakerdeck.com/jakewharton/simple-http-with-retrofit-2-droidcon-nyc-2015

https://github.com/square/retrofit/blob/master/CHANGELOG.md

@cosic lgtm except some issues I left comments about.

:+1: lgtm


Develop

lock sftp emailing bit on data lollipop ,virtualy remove all file prop. to web and delete using both hardware&format .

Garbage PR from likely a bot account, blocking going forward.

9
10insertp -win599
11
12
13
14
15
16
16
@@ -0,0 +1,16 @@

{
// Use IntelliSense to
learn about possible attributes.
//win { pwin10 ()  : ll / ll
descriptions of existing
attributes.
// For more information,
visit : https://go.microsoft.com/fwlink/?linkid= 830387
"version" : "0.2.


Updating sessionAuthenticated for Octane

The documented version of sessionAuthenticated was no longer working under Ember Octane. Using the new super keyword as documented here worked.

Closing this since sessionAuthenticated on the application route doesn't exist anymore in the latest version of ESA.

Sorry for the slow response and thanks for the effort!


Update for new governance

This starts updating the website for the new governance
This is related to https://github.com/jupyter/governance/pull/150, which updates the governance docs.

I also added a few badges for the social media links.

http://jupyter.org/governance/executive_council.html and http://jupyter.org/governance/software_steering_council.html still say that the EC and SSC have yet to be formed; we need to move these out of the "future governance" section and remove the "not yet formed" language"

http://jupyter.org/governance/executive_council.html and http://jupyter.org/governance/software_steering_council.html still say that the EC and SSC have yet to be formed; we need to move these out of the "future governance" section and remove the "not yet formed" language"

That (and many other things) is taken care of in https://github.com/jupyter/governance/pull/150

@echarles, @rpwagner, @ibdafna - can you upload or tell us where to find 160x160 pixel pictures of you to go on the About page of the new Jupyter website under the software steering council section? Perhaps easiest is just making a comment here and attaching your picture to the comment.
(And even if we merge this before getting your pictures, it would be easy to add your pictures later if you want.)
Also, @ivanov - I noticed your affiliation still says "Noteable" - do you want to update that, and if so, what should it read?

You can get mine on https://avatars.githubusercontent.com/u/226720?v=1&s=160


Refactor XLNet interface

Requested by Zhiting's comments in PR in texar-tf
Make the interface of XLNetEncoder be consistent with other modules.

Looks good. I'm thinking, would this problem be solved if we have a mechanism that can:

Add methods that is called prior to __init__ (of the uppermost subclass).
Add methods that is called after __init__ (of the uppermost subclass).

I feel that such mechanism could solve both this problem and the repeated-hparams initialization problem we've discussed before.
A hacky way of doing this is via metaclasses. When an instance of a class is created, the metaclass __call__ method is invoked, which internally calls the class __new__ and class __init__ methods. We can create a custom metaclass for ModuleBase that constructs the hparams object before __init__, and allows sub-metaclasses to append method calls after __init__.
A diagram of instance creation is as follows, taken from this very good article that explains it all:
`

Thanks a lot. I think this modification is related to #41 I will think about it.

Why is this PR related to "repeated-hparams initialization"?  In particular, what's the init argument  in the XLNetEncoder __init__ for in the first place?

It's because these two problems have similar root causes.
The init argument. Our pre-trained mixin interfaces requires the concrete classes to call init_pretrained_weights() at the end of their __init__ methods. This method is used to initialize the weights of the registered module parameters from the checkpoint file.
XLNetEncoder, which inherits PretrainedXLNetMixin, follows this pattern. However, XLNetDecoder inherits XLNetEncoder (which is not a good design; but it works at least for now), but has an extra parameter lm_bias that has to be registered before calling init_pretrained_weights(), which happens with the super().__init__ call. Due to PyTorch implementations, we can't register parameters before super().__init__ (which internally calls nn.Module.__init__), so we had this init argument to control whether we call init_pretrained_weights() in XLNetEncoder.__init__.
Relation to repeated-hparams creation. The hparams issue was that: hparams is created in ModuleBase.__init__, which will be called in super().__init__ of our built-in modules. However, certain base classes require additional arguments in their constructors (e.g., DataBase require a data_source argument), and some arguments cannot be constructed without knowing hparams values. As a results, the hparams object is constructed multiple times.
The init issue above could benefit from being able to add method calls (a call to init_pretrained_weights()) at the end of object initialization. The hparams issue could similarly benefit from being able to add calls before initialization (a call to construct hparams).

Thanks for explaining, and the possible solution.
The solution can be a candidate we can apply at some point. Since it's a bit intricate, for now (when the issue has not widely occurred), let's just work around case by case.
One of our interface design "principles" could to some extent (not completely) avoid the issue: put hyperparameters in hparams instead of constructor arguments whenever possible. In this way, it's in general unlikely (though not impossible) that an hyperparam is in the hparams of a class but at the same time is an argument of super().__init__
It looks the CharCNN example in the issue https://github.com/asyml/texar-pytorch/issues/41 is out of the scope of the above principle though. It's reasonable that in_channels is Conv1DEncoder.__init__ argument and char_embed_dim is in CharCNN hparams.

Yes, we could leave this for the future.
While the issue in the CharCNN example could be avoided with this principle, it only applies to values that fits in hparams -- and a data source is probably not one of them. There could also be logic that has to be done before calling the super class constructor.


test: add util to test same scenario for null or undefined

Issue or need
There are several unit tests around testing same thing in case of null or undefined. Starts being repetitive

Proposed changes
Introduce a util to avoid repeating this around.

Quick reminders

🤝 I will follow Code of Conduct
✅ No existing pull request already does almost same changes
👁 Contributing docs are something I've taken a look at
📝 Commit messages convention has been followed
💬 TSDoc comments have been added or updated indicating API visibility if API surface has changed.
🧪 Tests have been added if needed. For instance, if adding new features or fixing a bug. Or removed if removing features.
⚙ API Report has been updated if API surface is altered.

#922  👈
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Docs: Cleanup - Cleanup devlang from code blocks removes return character

Ran this on dotnet/docs repo. It doesn't appear to happen on all lanuges, but primarily ones fixing the csharp tags
AB#301102

Looks like it's probably this https://github.com/microsoft/vscode-docs-authoring/blob/6e143ffe7175d0b389dbe553df1539266f795403/packages/docs-markdown/src/controllers/cleanup/devlangsInCodeBlocks.ts#L49-L50
where the regex matches on \s at the end, but doesn't add any back in the replacement


colour ploints by intensities in plot_latent

Hello to all,
I'm writing to ask if there is any possibility to colour my points in latent plot by vector of intensities (numbers) corresponding to each point and add intensity scale.
I just found below options:
plot_latent(model, labels=None, which_indices=None,resolution=50, ax=None, marker='o', s=40, fignum=None, plot_inducing=False, legend=True, aspect='auto', updates=False)
Please let me know if you have any idea.
Best !

You can plot the points directly using the plot_scatter function. I believe by supplying an array to colour there and set the labels to false, it will plot the colours given by the array.

Dear @mzwiessele thank you for your response, indeed that's what I am doing now. I thought however plot_latent can have some additional option. Thanks !


Clarify Form Labels rule

In implementing the checks for Form Labels (#27) I had a question about the title attribute rule. In the examples under "Fail" we see:
<input type="text" name="name" title="Name" />
<input type="text" name="email" title="Email" />

Yet these both have a title attribute. I'm wondering why they're supposed to fail? Is the rule that the title attribute is only OK if there's only one field in the form?

A title attribute to label a form field is acceptable if there is only one field other than input[type=hidden,submit,reset,image]
Pass
<form action="#">
    <input type="hidden" name="token" value="qwert1234">
    <input type="text" name="name" title="Name">
    <input type="submit" value="Submit">
</form>

Fail
<form action="#">
    <input type="hidden" name="token" value="qwert1234">
    <input type="text" name="name" title="Name">
    <input type="text" name="email" title="Email">
    <input type="submit" value="Submit">
</form>


Specify allowOverlap between 2 specific views

Right now you can only specify that you want a view to ignore any views overlapping it. However, it would be useful to say that you only allow an overlap of 2 specific views. This way you can catch any unwanted overlaps.

Did you find any way to achieve this?

I unfortunately have not taken the time to try and implement this. This would be a nice feature to add though. I'm pretty sure it should be doable.


Implement shibboleth support

The cas-shibboleth project should contain a stock cas server set up using the maven overlay method with the modifications described at:
https://wiki.shibboleth.net/confluence/display/SHIB2/Shibbolize+a+CAS+server
Setting up a cas server using the maven overlay method is described at https://wiki.jasig.org/display/CASUM/Best+Practice+-+Setting+Up+CAS+Locally+using+the+Maven+WAR+Overlay+Method. This is the method that our existing cas project uses.
Once you have a stock cas server created, do everything described in the Shibbolize a CAS server wiki page prior to the Shibboleth Specifics section.
The cas-shibboleth project should be a drop-in replacement for the cas project for a situation in which Eureka and/or i2b2 are going to use shibboleth for authentication.

I'm declaring this completed and closed now that we have the casshib package. We'll create separate issues for any bugs that are encountered.


Logic Error in experimental Unity Plugin HelloTFLite.cs Sample Code

Issue type
Documentation Bug
Have you reproduced the bug with TensorFlow Nightly?
No
Source
binary
TensorFlow version
tf 2.15
Custom code
No
OS platform and distribution
Windows 11
Mobile device
No response
Python version
No response
Bazel version
No response
GCC/compiler version
No response
CUDA/cuDNN version
No response
GPU model and memory
No response
Current behavior?
Currently in HelloTFLite.cs in the experimental Unity Plugin example project there is a logic error at line 59
Here is the function i am looking at
  void Start () {
    Debug.LogFormat("TensorFlow Lite Verion: {0}", Interpreter.GetVersion());

    var options = new Interpreter.Options() {
      threads = 2,
    };
    interpreter = new Interpreter(model.bytes, options);

    int inputCount = interpreter.GetInputTensorCount();
    int outputCount = interpreter.GetOutputTensorCount();
    for (int i = 0; i < inputCount; i++) {
      Debug.LogFormat("Input {0}: {1}", i, interpreter.GetInputTensorInfo(i));
    }
    for (int i = 0; i < inputCount; i++) {
      Debug.LogFormat("Output {0}: {1}", i, interpreter.GetOutputTensorInfo(i));
    }
  }

In the second for loop the bound inputCount should be outputCount as it is looping through the output tensors
Standalone code to reproduce the issue
Load in a model with input and output tensors of different length and you will find that either not all the tensors get logged or there is an error.

Relevant log output
No response

Hi @Tom-James-Marsden,
I have gone through the file and raised a PR. Please track the PR #63131.
Thank You

Even though this is such a tiny bug in some experimental code from a project that isn't going to be gone further with I'm dead excited I got to point out and help fix a part of this repository. Whoop whoop


Shift lines affected by .wrap() for less flat text layouts

The feature could work like this:
scribble_element.wrap(maxWidth, [maxHeight], [characterWrap], [lineShift]);

-----------------------

Example:

scribble("Hello world, how are you?").wrap(40, -1, false, 10);

Hello
     world,
         how are
                you?

lineShift would shift by a specific amount every new wrapped line relatively to the previous one.

The feature could also be its own method to allow for even more customization without bloating the .wrap() method.
scribble_element.wrapShift(shift1, [shift2] ...);

-----------------------

Example:

scribble("Hello world, how are you?").wrapShift(40,-20);

       Hello
              World
    how are
you?

Where the last argument would affect every line going down if no more arguments are provided

This does also raise the possiblity of a .lineWidthFunc() method for irregular-shaped containers.


Switch to the byteme library for handling file inputs.

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Deprecate on_keyboard_interrupt callback hook

What does this PR do?
This callback hook will be subsumed by the new on_exception hook (PyTorchLightning#9183).
The PR includes small addition to the is_overridden helper function, to automatically set the parent to Callback if a Callback instance is passed, which made changes to configuration_validator.py simpler.
Does your PR introduce any breaking changes? If yes, please list them.
Before submitting

[x] Was this discussed/approved via a GitHub issue? (not for typos and docs)
[x] Did you read the contributor guideline, Pull Request section?
[x] Did you make sure your PR does only one thing, instead of bundling different changes together?
[ ] Did you make sure to update the documentation with your changes? (if necessary)
[x] Did you write any new necessary tests? (not for typos and docs)
[x] Did you verify new and existing tests pass locally with your changes?
[ ] Did you list all the breaking changes introduced by this pull request?
[x] Did you update the CHANGELOG? (not for typos, docs, test updates, or internal minor changes/refactorings)

PR review
Anyone in the community is welcome to review the PR.
Before you start reviewing make sure you have read Review guidelines. In short, see the following bullet-list:

[x] Is this pull request ready for review? (if not, please submit in draft mode)
[x] Check that all items from Before submitting are resolved
[x] Make sure the title is self-explanatory and the description concisely explains the PR
[x] Add labels and milestones (and optionally projects) to the PR so it can be classified

Did you have fun?
Make sure you had fun coding 🙃

Waiting to merge - will incorporate fix for #9286

Waiting to merge

there are still some failing tests, mind have look?


Allow SocketCommunicator revocation to interrupt calls to _receive()

In hindsight this doesn’t seem as useful as I originally thought.  The main benefit would be getting other players’ attention if they’re using longer timeouts than the player initiating the revocation.  Examples where this would be likely to happen seem to be pretty contrived, and would most likely involve subsets of players, which calls-out for separate communicators anyway.


TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'

Getting type error on the current Commit.
Using Theano backend.
Using gpu device 6: GeForce GTX TITAN X (CNMeM is enabled with initial size: 90.0% of memory, CuDNN 4004)
/home/anaconda3/lib/python3.5/site-packages/theano/tensor/signal/downsample.py:5: UserWarning: downsample module has been moved to the pool module.
warnings.warn("downsample module has been moved to the pool module.")
Running model:  tradcom
Traceback (most recent call last):
File "UFCNN1.py", line 623, in
loss="categorical_crossentropy", sequence_length=sequence_length, optimizer=sgd )
File "UFCNN1.py", line 215, in ufcnn_model
init)
File "UFCNN1.py", line 131, in ufcnn_model_concat
model.add_node(Convolution1D(nb_filter=nb_filter, filter_length=filter_length, border_mode='valid', init=init, input_shape=(sequence_length, features)), name='conv1', input='input_padding')
File "/home/anaconda3/lib/python3.5/site-packages/keras/layers/containers.py", line 359, in add_node
layer.set_previous(self.nodes[input])
File "/home/anaconda3/lib/python3.5/site-packages/keras/layers/core.py", line 98, in set_previous
assert self.input_ndim == len(layer.output_shape), ('Incompatible shapes: layer expected input with ndim=' +
File "/home/anaconda3/lib/python3.5/site-packages/keras/layers/convolutional.py", line 707, in output_shape
input_shape[1] + self.padding * 2,
TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'

Works on Python 2.7, Python 3.5 on CPU with latest master branch of Keras.
Please check.

Upgraded Keras 0.3.2 master branch from the source

Issue resolved


Diagnose filtering issue

The query filtering is not working as expected. For example, issuing the following GraphQL query will not correctly filter the list:
  listStrains(input: { limit: 10, filter: "species==='Dictyostelium purpureum'" }) {
    strains {
      id
      label
      species
    }
  }

The result just provides a list of all strains like so:
{
    "id": "DBS0351367",
   "label": "myoB-/[act15]:myoB(S332A)",
   "species": "Dictyostelium discoideum"
},

The issue appears to be when a filter contains a space. For example, changing the filter to filter: "species~purpureum" returns the correct set of results.
It's possible that the filter statement is not getting parsed and/or generated properly in arangomanager. However, need to follow the chain of logic to properly diagnose.

It is likely that the RegEx check needs to be updated in arangomanager. It is not currently allowing for white spaces in the query. We also likely need to update it to allow for other characters such as [ and ] which are commonly used in strain descriptors.


update documentation on configuration parameters

There are parameters in Configuration.java that are not described in the documentation. It is necessary to review them, describe their purpose or remove them.

reviewed and described the most important. some of them were removed from the doc

Verified, fixed.


Support GraphQL variables

Adds support for GraphQL variables in a GraphQL body translation.
Adds new test cases for GraphQL bodies.
There's also a live example that can be run against the GitHub API. It pulls a few repo names:

node bin/postman-to-k6.s example/v2/github-graphql.json >test.js
In GitHub developer settings grab a personal access token, one with repo access. Paste it as the value of GITHUB_TOKEN at the top.
k6 run test.js

It should print an info line with an object like this:
{"data":{"viewer":{"name":null,"repositories":{"nodes":[{"name":"ulid"},{"name":"gojay"},{"name":"yaegi"}]}}}}

Closes #38.

Have tested this and works great. Merging. Thanks @bookmoons!

Thanks!


queryDns(): [ringbalancer] querying dns for app_backend failed: dns server error: 3 name error

but I have already delete the upstream app_backend, why logs appear this

@inewlife please do not create an issue like this. There is a template that lists some extra info for us to help you out in resolving your problems. Creating an issue with just a title has little to no useful information.
All I can tell you in this situation is that the error "3 name error" has two possible causes, both originating from your dns server:

there was no record by the requested name (the error is generated b y the dns server, not by Kong)
a record was returned but didn't contain the requested name


Support esbuild metafile generation

Requests

https://serverless-stack.slack.com/archives/C01HQQVC8TH/p1640695656172700

We are transition this repo to https://github.com/sst/v2 and are closing this issue for now. If it is still relevant please reopen it there - sorry for the trouble


Allow this app to load additional sass files

Some users may want to customize their site beyond what can be done by changing bulma variables. For this, we could offer the option of loading additional sass files. I'm not sure how best to do this, so I'm inviting anyone reading this to discuss it in this issue. Here are a couple of potential ways:

Take a new BULMA_SETTINGS configuration parameter called additional_sass, which is a list of PosixPaths pointing at additional sass files that django-simple-bulma should load along with bulma. This means it would add that css onto the already huge css file that bulma + extensions makes, so it's not a very optimized solution, but since most users probably won't be adding more than a couple of lines of their own sass anyway, that might be okay.

Tell the user to put their .sass files in a specific location ($root/static/sass/ or something) and then compile all the files in this folder to css files of the same name whenever collectstatic is run. Then the user would manually load these by just using {% static "css/mycoolfile.css" %}. Saves the user the hassle of dealing with libsass directly, but isn't as smooth as just loading it with that {% bulma %} tag.

Tell the user to put all their desired additional sass into a specific file in a specific location, like $project_root/static/bulma_additional.sass. Then just import that file at the end of the bulma.sass. This is pretty easy and less error prone, but might be messy if the user needs a lot of sass. Again, though, I think that's probably rare.

This feels a little too feature-creepy to me. I kinda feel like this belongs in another package? But there's already plenty that do this already, right?

https://github.com/jrief/django-sass-processor/ actually this looks great. I guess you're right regarding feature creep.


Asurascans

Source name
Asurascans
Source link
https://asuratoon.com/
Source language
English
Other details
Please can you add this too. They have really good translations. I mistakenly removed mine. 🙏
Acknowledgements

[X] I have checked that the extension does not already exist on the website extensions list or the app.
[X] I have checked that the extension is not on the removed sources list.
[X] I have searched the existing issues and this is a new ticket, NOT a duplicate or related to another open or closed issue.
[X] I have checked that the extension does not already exist by searching the GitHub repository and verified it does not appear in the code base.
[X] I have written a meaningful title with the source name.
[X] I will fill out all of the requested information in this form.

I've just restored all removed extensions and added them to this repo, including yours.
If the extensions don't appear in the app yet, you should clear the app cache and refresh the extension list again.


CuPy.random.randn supports dtype parameter but numpy.random.randn does not

^
This is a problem because we want 100% API compatibility; not only should numpy code always work in CuPy, CuPy code should also always work on numpy.

Hmm, I added this option to provide an easy way to use the float32 support of cuRAND, which benefits for certain situations (see, for example, gaussian function). CuPy does not support 100% of the NumPy APIs (e.g. some CuPy functions lack options supported by NumPy), so I want to tolerate reverse situations.

Ok I see. I guess we can leave this, since really numpy should add a dtype parameter for this.. In general though, shoudn't the end goal be to make cupy 100% compatible with numpy?

Ideally, yes. I agree that the ultimate goal of the CuPy ndarray interface is the 100% compatibility with NumPy (of course except low-level features like custom kernel generation and ctypes support, which definitely must be different). Though, there might be situations that NumPy design is not suited to avoid overheads on GPU computation. In such case, we have to provide a more efficient way outside of the NumPy interface. It might be helpful for host/device-agnostic coding to provide wrapper functions for such case that can be used for both NumPy and CuPy (e.g. in the case of #522, providing add_dot that works both for numpy.ndarray and cupy.ndarray).


Styling selected calendarDay

Hi,
I was wondering if custom styling the selected start and end date like this is possible with this package:

This is what I tried:
.CalendarDay__selected_end {
    width: 34px;
    height: 34px;
    background: #bfc849;
    opacity: 0.5;
    border: 0px;
    padding: 0px;
    border-top-right-radius: 50%;
    border-bottom-right-radius: 50%;
}

.CalendarDay__selected_start {
    width: 34px;
    height: 34px;
    background: #bfc849;
    opacity: 0.5;
    border: 0px;
    padding: 0px;
    border-top-left-radius: 50%;
    border-bottom-left-radius: 50%;
}

// Will edit selected date or the endpoints of a range of dates
.CalendarDay__selected {
    background: #bfc849;
    color: white;
    opacity: 1;
    position: relativet;
    z-index: 1;
    border-radius: 100%;
}

But then I just end up with this:

This happens since the .CalendarDay__selected overwrites the other two classes. Is there a way of getting the desired result?

With some help I managed to get it working by using the ::before pseudo element.


Cloud communication API limits in Microsoft Graph per tenant ?

Hi,
The question is simply about the scope of limit the Cloud communication API.
is it a limit per Bot/ application or per tenant ?
Considering thecase of a multi tenant app, what would be the max number of call the application can handle per tenant and in total ?
Same question regarding conccurent calls.
Thx !

Hi @VinodRavichandran,
may be you can help ? :)
Thx !

@ananmishr

I also want to know the max number of calls/tenant.

Hi @ananmishr, @VinodRavichandran ,
Any  feedback on this please ?
Thx

Hi @vinaychandra @ananmishr,
The API here states limit for call is 10 000 per app per tenant.
if we have 2 app instance for a given tenant, how do we calculate the limit? is the 10 k shared between instances or 10k per instance ?
Thx in advance !


Add search

Add back search functionality.
This also fixes analytics and some minor mobile styles.

lgtm
Thank you so much for the PR!


Update Azure WAAgent to latest release

We currently ship WAAgent 2.2.32 which will be deprecated starting May 2020 (https://support.microsoft.com/en-us/help/4049215/extensions-and-virtual-machine-agent-minimum-version-support). Update WAAgent to the latest upstream release (2.2.46 at the time of writing: https://github.com/Azure/WALinuxAgent/releases ) for the Azure platform.

Since OEM partitions are not updated (see https://github.com/flatcar-linux/Flatcar/issues/21) it would be good to not just bump the version because it does not solve our problem and just delays it.
We should containerize the service with a unit on /usr that is started under the condition that the Azure OEM ID is in the kernel command line.

Eventually yes, but the version bump is on a schedule (Microsoft will deprecate the version currently shipped in May). I would like to prevent for the containerisation to be on a schedule.

First try in https://github.com/flatcar-linux/coreos-overlay/pull/245

Stable 2345.3.1 and Beta 2411.1.1 were just released, so this issue should be fixed.
Alpha and Edge are still with the older version of WAAgent.

No, that was not part of the Stable and Beta releases because it landed later. It will be in all new releases, however.

@dongsupark @pothos  Alpha and Edge should ship the updated version so we can stabilise this (move to Beta and then Stable in successive releases) before Microsoft deprecates the version currently used in Stable on May 1st.

Implemented in https://github.com/flatcar-linux/coreos-overlay/pull/245, will be included in the next Alpha and Stable. Thank you!

wa-linux-agent was updated to 2.2.46 for for Alpha 2466.0.0 and Edge 2466.99.0.
Will leave the issue open, as Stable and Beta are not updated yet.

Stable 2512.2.0 or newer already has wa-linux-agent 2.2.46.


Add support for Valve Source Engine 2 using...

this plugin https://github.com/H2xDev/GodotVMF

It's a really cool plugin, but it's very different from FuncGodot to the point where I don't see being able to feasibly integrate their processes into FuncGodot's. We'd need a different design to support VMF, it's unfortunately not as simple as slapping another plugin onto FuncGodot.


How to add skip to 10 seconds forward/backward in video Button around BigPlayButton ?

Any reference to documentation is also appereciated

Hello @sanjampreet-singh ,
Here's the UI tutorial.
You can create custom elements and add them to the UI.

Hello @sanjampreet-singh ,
Here's the UI tutorial.
You can create custom elements and add them to the UI.

Yes, I do watched this example already but was not able to follow same...
Could you please insist providing details of functions or classes provided by shaka say to seek 10seconds forward on button click or something like that...

Yes, I do watched this example already but was not able to follow same...
Could you please insist providing details of functions or classes provided by shaka say to seek 10seconds forward on button click or something like that...

Would you please tell us what didn't work for you? We'd love to know what we can improve on our tutorials.
We will add a button to seek 10seconds forward in the future! Meanwhile, we also welcome contributions to implement that from the community.

Would you please tell us what didn't work for you? We'd love to know what we can improve on our tutorials.
We will add a button to seek 10seconds forward in the future! Meanwhile, we also welcome contributions to implement that from the community.


[BUG][iOS] Error while initializing session on a real device

Describe the Bug
I am receiving error while initializing a session on a real iOS device, however; on a simulator it works fine.
Repro Steps
Honestly, I have no idea if it's my device's fault and don't know if it can be reproduced.
Expected Behavior
It should initialize a session successfully.
Screenshots
None.
Project Info
o0hu85shfh
Platform/Framework Info

Device: iPhone 13 Pro
OS: iOS 16.0
Application Framework: React Native
Clarity Version: 3.0.2

Additional Context
2024-09-09 20:51:56.888652+0200 MyApp[68191:19867679] Task .<6> finished with error [-1000] Error Domain=NSURLErrorDomain Code=-1000 "bad URL" UserInfo={_kCFStreamErrorCodeKey=22, NSUnderlyingError=0x282eed7a0 {Error Domain=kCFErrorDomainCFNetwork Code=-1000 "(null)" UserInfo={_NSURLErrorNWPathKey=satisfied (Path is satisfied), interface: en0, ipv4, dns, _kCFStreamErrorCodeKey=22, _kCFStreamErrorDomainKey=1}}, _NSURLErrorFailingURLSessionTaskErrorKey=LocalDataTask .<6>, _NSURLErrorRelatedURLSessionTaskErrorKey=(
"LocalDataTask .<6>"
), NSLocalizedDescription=bad URL, NSErrorFailingURLStringKey=https://www.clarity.ms/tag/mobile/o0hu85shfh, NSErrorFailingURLKey=https://www.clarity.ms/tag/mobile/o0hu85shfh, _kCFStreamErrorDomainKey=1}
2024-09-09 20:51:56.940421+0200 MyApp[68191:19867290] [Clarity] D/ Capturing frame 1.
It is the only Clarity error from the console.

Closing. It was an issue with my custom DNS. It was blocking Clarity's URLs.


Gen choose fails with stream of instances of generic interface

Problem statement
Stream<Supplier<String>> strings = Stream.of(() -> "test", () -> "test2");
Property.def("Test")
         .forAll(Gen.choose(strings).arbitrary())
         .suchThat(s -> true)
         .check()
         .assertIsSatisfied();
}

fails with following stack trace:
Nov 22, 2016 1:46:12 AM org.junit.platform.launcher.core.ServiceLoaderTestEngineRegistry loadTestEngines
INFORMATION: Discovered TestEngines with IDs: [junit-jupiter]

java.lang.ArrayStoreException
	at java.lang.System.arraycopy(Native Method)
	at java.util.ArrayList.toArray(ArrayList.java:408)
	at javaslang.Value.toJavaArray(Value.java:489)
	at javaslang.test.Gen.choose(Gen.java:205)
...

Possible cause
This exception is thrown if the runtime type of the specified array is not a supertype of the runtime type of every element in this list (see JavaDoc). I assume the choose method of Gen to be the culprit
final T[] array = stream.toJavaArray((Class<T>) stream.head().getClass());

Although Supplier<String> is a supertype of stream.head() the actual type of stream.head() is something like test.Clazz$$Lambda$120/90205195. In method toJavaArray of interface Value
this type is used to indicate the component type of the resulting array:
final java.util.List<T> list = toJavaList();
return list.toArray((T[]) java.lang.reflect.Array.newInstance(componentType, list.size()));`

The type is correct for the first element, but not for the second. If the second Supplier is removed from the Stream, the test succeeds.
Stream<Supplier<String>> strings = Stream.of(() -> "test");
Property.def("Test")
         .forAll(Gen.choose(strings).arbitrary())
         .suchThat(s -> true)
         .check()
         .assertIsSatisfied(); // works fine
}

Solution proposals

Use TypeTokens if appropiate
Add new choose method with additional class parameter

Gen.choose(strings, Supplier.class) // example

Hi @gtrefs,
thank you for you detailed bug description - it helped me going straight to the cause of the problem.
I think the following solution fits best because it is minimal invasive. It does work for your test above:
Buggy version
static <T> Gen<T> choose(Iterable<T> values) {
    Objects.requireNonNull(values, "values is null");
    final Stream<T> stream = Stream.ofAll(values);
    if (stream.isEmpty()) {
        throw new IllegalArgumentException("Empty iterable");
    }
    @SuppressWarnings("unchecked")
    final T[] array = stream.toJavaArray((Class<T>) stream.head().getClass());
    return choose(array);
}

Fixed version
static <T> Gen<T> choose(Iterable<T> values) {
    Objects.requireNonNull(values, "values is null");
    final Iterator<T> iterator = Iterator.ofAll(values);
    if (!iterator.hasNext()) {
        throw new IllegalArgumentException("Empty iterable");
    }
    @SuppressWarnings("unchecked")
    final T[] array = (T[]) iterator.toJavaArray();
    return choose(array);
}

Also I realized that the javaslang-test package was written before we had javaslang.collection.Iterator. We can substitute (some) usages of Stream now with Iterator. I will create an issue to improve that.
If you do not find anything that is still in our way, could you please create a PR containing the fix sketched above?
Many thanks!

(off-topic: I did the Iterator optimizations in #1700)

Ah... nice :). I did not find anything else. I will create a PR later this evening.


Currency scrollbar affects the transaction scrollbar

Currency scrollbar affects the transaction scrollbar:
https://user-images.githubusercontent.com/69896204/114845693-a5851a00-9de4-11eb-96c2-cee170351249.mov

I'm not sure, but it looks like a reasonable behavior: the whole page is scrolled after the nested component is scrolled till the end.

I'm not sure, but it looks like a reasonable behavior: the whole page is scrolled after the nested component is scrolled till the end.

in that case, this is not an issue.