text:
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 notifications@github.com 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

authors: alipirani88 katiesaund sthiede


text:
PP: Need to work out how we serve the need for applying for multiple permits

@kaydale Could you write some info about this please? I think you've thought about it a lot more than I have.

Actually this is a duplicate of #33 - Let's add thoughts there

source: gharchive/issue

repo: alphagov/verify-local-patterns

license: MIT

license_type: permissive

license_source: github-api


text:
Correction in performance graphs, swapped labels for Decode and Transport

Nvm, big merge conflict on my old version. I'll redo this

source: gharchive/pull-request

repo: alvr-org/ALVR


text:
Improve style on default pages

#20

repo: amilochau/MilNode


text:
Replaced a Visual remap to a more useful one

Thanks, I'll update the readme.

authors: UtkarshChemE amix

repo: amix/vimrc

license: mit

license_source: bigquery


text:
skeleton

Codecov Report

Merging #95 into master will not change coverage.
The diff coverage is n/a.

@@            Coverage Diff            @@
##            master       #95   +/-   ##
=========================================
  Coverage   100.00%   100.00%
=========================================
  Files            1         1
  Lines            2         2
=========================================
  Hits             2         2

Continue to review full report at Codecov.

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text:
Xreffixes

Codecov Report

Merging #730 into master will increase coverage by 0.7%.
The diff coverage is 95.55%.

@@            Coverage Diff            @@
##           master     #730     +/-   ##
=========================================
+ Coverage   72.72%   73.42%   +0.7%
=========================================
  Files          51       51
  Lines       16145    18129   +1984
=========================================
+ Hits        11742    13312   +1570
- Misses       4403     4817    +414

Impacted Files
Coverage Δ

tests/test_analysis.py
99.53% <100%> (+0.06%)
:arrow_up:

androguard/core/analysis/analysis.py
77.45% <89.47%> (+0.63%)
:arrow_up:

androguard/core/bytecodes/dvm.py
68.21% <0%> (+4.94%)
:arrow_up:

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authors: codecov-io reox

repo: androguard/androguard


text:
Reparse version 3

@aolieman Your changes can be seen here. I pulled them manually and merged them with the other changes into the develop branch.
This is a continuation of #4

repo: andychase/reparse


text:
Fix link to consoleDir.coffee

arf thanks!
Some work has to be pushed in the doc (hopefully soon)

authors: andypetrella nightscape

repo: andypetrella/spark-notebook


text:
prototype(radio): 3.5 Set up the MDC foundation

Is there anything preventing this from being merged?

repo: angular/components


text:
Upgrade fail

@petebacondarwin I don't understand what you're attempting here. This QuickStart is not intended to support Angular 1 or NgUpgrade. Closing for that reason. Discuss with me offline if you want to pursue.

@wardbell - no problem. This was demonstrating to @Foxandxss how to fix his problem. The original upgrade-fail branch on this repo was his demonstration of his problem.

My bad, I Was using this repo for testing approaches.

authors: Foxandxss petebacondarwin wardbell

repo: angular/quickstart


text:
Line and character offset are 0 based, so add 1.

The build failures are a fluke, I believe.


text:
add unit test and fixes for ANStorageModel

Current coverage is 69.59% (diff: 100%)

Merging #6 into master will increase coverage by 0.32%

@@             master         #6   diff @@
==========================================
  Files            63         63
  Lines          2222       2223     +1
  Methods         420        420
  Messages          0          0
  Branches        163        165     +2
==========================================
+ Hits           1539       1547     +8
+ Misses          683        676     -7
  Partials          0          0

Powered by Codecov. Last update 642f525...0dc0d78

authors: codecov-io oks

repo: anodamobi/Alister


text:
NO-JIRA review docs for content, style, & format

Nice!!!! nice job!

authors: clebertsuconic jbertram

repo: apache/activemq-artemis


text:
Update year to 2016

Update to LICENSE and NOTICE based on would be bundled in a release (i.e. a zip of the git repo).

repo: apache/apache-website-template


text:
ARROW-6437: [R] Add AWS SDK to Homebrew formulae

@ursabot crossbow submit homebrew-cpp homebrew-cpp-autobrew

@ursabot crossbow submit homebrew-cpp-autobrew

repo: apache/arrow


text:
ARROW-7892: [Python] Add FileSystemDataset.format attribute

Let's wait here on the Source/Dataset PR, to avoid rebasing problems for @bkietz in the cython code

Rebased this after the Dataset/Source merge, this now adds a format attribute to the FileSystemDataset class.


text:
Update LICENSE dependencies to current project state

👍 merging

authors: geomacy neykov

repo: apache/brooklyn


text:
CAMEL-8194: Allow camel-elasticsearch to work in an OSGi environment - port to 2.15.x

Thanks for this PR. It has been merged. Do you mind closing this.

Thanks for the PR this has been merged. Do you mind closing this?

Closed, thanks for the reminder.

repo: apache/camel


text:
[FLINK-2444] add tests for HadoopInputFormats

3 builds failed:

one due to FLINK-2719 (log)
one due to a failure in JobManagerFailsITCase (log)
one due to a build failure in the flink-ml module (log)

Hi @mliesenberg, sorry for the late review. Tests look really good.
I think there is one auto-completion error in the code (see inline comment).
I will run a build on my Travis to check for the failing tests.
Thanks, Fabian

thanks for the review, addressed the comment, squashed and rebased on master

Found just a few style issues. Otherwise good to merge.

Thanks for the quick update. Will merge this PR

authors: fhueske mliesenberg

repo: apache/flink


text:
[FLINK-5486] Fix lacking of synchronization in BucketingSink#handleRe…

lgtm

Tests run: 6, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 91.985 sec <<< FAILURE! - in org.apache.flink.test.checkpointing.ExternalizedCheckpointITCase
testExternalizedFullRocksDBCheckpointsStandalone(org.apache.flink.test.checkpointing.ExternalizedCheckpointITCase)  Time elapsed: 29.976 sec  <<< ERROR!
java.io.IOException: java.lang.Exception: Failed to complete checkpoint
	at org.apache.flink.runtime.testingUtils.TestingCluster.requestCheckpoint(TestingCluster.scala:399)
	at org.apache.flink.test.checkpointing.ExternalizedCheckpointITCase.testExternalizedCheckpoints(ExternalizedCheckpointITCase.java:218)
	at org.apache.flink.test.checkpointing.ExternalizedCheckpointITCase.testExternalizedFullRocksDBCheckpointsStandalone(ExternalizedCheckpointITCase.java:78)
Caused by: java.lang.Exception: Failed to complete checkpoint
	at org.apache.flink.runtime.testingUtils.TestingJobManagerLike$$anonfun$handleTestingMessage$1$$anon$2.apply(TestingJobManagerLike.scala:375)
	at org.apache.flink.runtime.testingUtils.TestingJobManagerLike$$anonfun$handleTestingMessage$1$$anon$2.apply(TestingJobManagerLike.scala:358)
	at org.apache.flink.runtime.concurrent.impl.FlinkFuture$5.onComplete(FlinkFuture.java:272)
	at akka.dispatch.OnComplete.internal(Future.scala:247)
	at akka.dispatch.OnComplete.internal(Future.scala:245)
	at akka.dispatch.japi$CallbackBridge.apply(Future.scala:175)
	at akka.dispatch.japi$CallbackBridge.apply(Future.scala:172)
	at scala.concurrent.impl.CallbackRunnable.run(Promise.scala:32)

Run QA again ?

Okay. Ted. I will trigger the QA soon.

triggering now....

retest this please

OKay. Thanks , Ted. Will retest again soon enough./

@tedyu I am retesting now......let us wait what will happen.

Thanks for your contribution. I have a few questions because the submitted code does not match with what the ticket currently says:
From https://issues.apache.org/jira/browse/FLINK-5486:

The handlePendingFilesForPreviousCheckpoints() call should be enclosed inside the synchronization block. Otherwise during the processing of handlePendingFilesForPreviousCheckpoints(), some entries of the map may be cleared.

I am confused because the submitted code encloses bucketState.pendingFilesPerCheckpoint.clear(); in a synchronized block.
@tedyu Did you run into actual production issues, or did you find the problem while reviewing the code? Can you elaborate why the additional synchronized block is needed?

I am closing this PR because FLINK-5486 got closed. Please reopen the ticket/PR if you disagree.

authors: GJL tedyu zhangminglei


text:
HADOOP-17505. public interface GroupMappingServiceProvider needs default impl for getGroupsSet()

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Private Build-1.8.0_282-8u282-b08-0ubuntu1~20.04-b08

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/usr/lib/jvm/java-11-openjdk-amd64:Ubuntu-11.0.10+9-Ubuntu-0ubuntu1.20.04 /usr/lib/jvm/java-8-openjdk-amd64:Private Build-1.8.0_282-8u282-b08-0ubuntu1~20.04-b08

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https://ci-hadoop.apache.org/job/hadoop-multibranch/job/PR-2661/1/testReport/

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modules
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https://ci-hadoop.apache.org/job/hadoop-multibranch/job/PR-2661/1/console

versions
git=2.25.1 maven=3.6.3 spotbugs=4.2.2

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These changes LGTM. Its been quite a long time since this patch was posted. @ayushtkn @xiaoyuyao have you any further comments or should we commit?

Thanks @ayushtkn @sodonnel

authors: hadoop-yetus sodonnel vinayakumarb

repo: apache/hadoop


text:
Ignite 2.1.4 p2

PR is not associated with a ticket. Apache Ignite issues are managed under Apache JIRA: https://issues.apache.org/jira/projects/IGNITE/
Please see how to associate ticket and PR in:
https://cwiki.apache.org/confluence/display/IGNITE/How+to+Contribute#HowtoContribute-Creation
Closing PR (which seems to be test-only) due to inactivity.
Feel free to reopen this PR if it is actual.

authors: dspavlov mcherkasov

repo: apache/ignite