Ingest wip to be added to other var db code #6582
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add pet creation to walker BRUH - cleanup the cword code update vet schema add headers enum and method to pet creation add xsv creation to loop update vet fix extra delim bug and show non-ref placeholder dont rebase me bruh Also fixed `[.....]` strings in the vet and converted a lot of strings to constants plus a couple of TODOs Fix GT String to output index of alleles instead of allele charaters fix enum bug add GQ band to drop as an optional param include end base code used to push PET and VET to BQ i dont know, it finally fuckign works....seriously. also schema jsons testing wip cleanup update schema and pray update schema cuz im bad added ability to pass in what GQ state to interpret as "missing" as well as skeleton for creating the metdata tsv (sample list, what interval list was use, the interval list's md5, and what GQ is signified by "missing". Also put some util files in a folder under BlahVariantWalkerUtils for now (should get rid of them eventually but nice to have for now) spacing + adding optional to GQ arguments (whoops) rename intervalListPath to intervalListBlob pass thru sample name swap out errors thrown add stringified interval list to metadata table fixup on interval blog rename use L for interval list This doesn't have the level of validation that we need, but works for now Ideally the interval list is required to be a picard interval list file wip testing to be dropped? interval wip add testing materials wip which type should this be passed in asg md5 interval list concated string wip split xsvs by contig add vet stripping intial changes review vet trim with Laura fix overzealous missing bug laura seal of approval on schema add back call_DP until we are sure evoq doesn't need it write chr dirs on the fly create dirs for chrs w pet and vet dirs inside add sample id to metadata semantics for sample id move position and sample into main method for easier access add sample id mapping and use it add enum for chr index use longs for the chr addition add array schema and enum add bool for array update array options with sample id and chr adjustment wip to remove chr separation new sample directory structure let the rename begin fixup on walker for arrays more renames better comments fixup on ingest walker
RoriCremer
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ahaessly
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Aug 13, 2020
* initial vet creation class * initial variant walker for jg * initial pet creation class add pet creation to walker update vet schema add headers enum and method to pet creation add xsv creation to loop update vet fix extra delim bug and show non-ref placeholder Also fixed `[.....]` strings in the vet and converted a lot of strings to constants plus a couple of TODOs Fix GT String to output index of alleles instead of allele characters fix enum bug add GQ band to drop as an optional param include end base code used to push PET and VET to BQ added ability to pass in what GQ state to interpret as "missing" as well as skeleton for creating the metdata tsv (sample list, what interval list was use, the interval list's md5, and what GQ is signified by "missing". Also put some util files in a folder under BlahVariantWalkerUtils for now (should get rid of them eventually but nice to have for now) spacing + adding optional to GQ arguments (whoops) rename intervalListPath to intervalListBlob pass thru sample name swap out errors thrown use L for interval list This doesn't have the level of validation that we need, but works for now Ideally the interval list is required to be a picard interval list file md5 interval list concated string wip split xsvs by contig add vet stripping intial changes review vet trim with Laura fix overzealous missing bug laura seal of approval on schema add back call_DP until we are sure evoq doesn't need it write chr dirs on the fly create dirs for chrs w pet and vet dirs inside add sample id to metadata semantics for sample id move position and sample into main method for easier access add sample id mapping and use it add enum for chr index use longs for the chr addition add array schema and enum add bool for array update array options with sample id and chr adjustment wip to remove chr separation new sample directory structure let the rename begin fixup on walker for arrays more renames better comments fixup on ingest walker * unrelated conflict--maybe merge mistake? * cleanup * swap method for indexed alleles * add genome specific VET creation * move mode enum into common code * wip on adding enums as params
ahaessly
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Sep 11, 2020
* initial vet creation class * initial variant walker for jg * initial pet creation class add pet creation to walker update vet schema add headers enum and method to pet creation add xsv creation to loop update vet fix extra delim bug and show non-ref placeholder Also fixed `[.....]` strings in the vet and converted a lot of strings to constants plus a couple of TODOs Fix GT String to output index of alleles instead of allele characters fix enum bug add GQ band to drop as an optional param include end base code used to push PET and VET to BQ added ability to pass in what GQ state to interpret as "missing" as well as skeleton for creating the metdata tsv (sample list, what interval list was use, the interval list's md5, and what GQ is signified by "missing". Also put some util files in a folder under BlahVariantWalkerUtils for now (should get rid of them eventually but nice to have for now) spacing + adding optional to GQ arguments (whoops) rename intervalListPath to intervalListBlob pass thru sample name swap out errors thrown use L for interval list This doesn't have the level of validation that we need, but works for now Ideally the interval list is required to be a picard interval list file md5 interval list concated string wip split xsvs by contig add vet stripping intial changes review vet trim with Laura fix overzealous missing bug laura seal of approval on schema add back call_DP until we are sure evoq doesn't need it write chr dirs on the fly create dirs for chrs w pet and vet dirs inside add sample id to metadata semantics for sample id move position and sample into main method for easier access add sample id mapping and use it add enum for chr index use longs for the chr addition add array schema and enum add bool for array update array options with sample id and chr adjustment wip to remove chr separation new sample directory structure let the rename begin fixup on walker for arrays more renames better comments fixup on ingest walker * unrelated conflict--maybe merge mistake? * cleanup * swap method for indexed alleles * add genome specific VET creation * move mode enum into common code * wip on adding enums as params
meganshand
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Oct 6, 2020
* initial vet creation class * initial variant walker for jg * initial pet creation class add pet creation to walker update vet schema add headers enum and method to pet creation add xsv creation to loop update vet fix extra delim bug and show non-ref placeholder Also fixed `[.....]` strings in the vet and converted a lot of strings to constants plus a couple of TODOs Fix GT String to output index of alleles instead of allele characters fix enum bug add GQ band to drop as an optional param include end base code used to push PET and VET to BQ added ability to pass in what GQ state to interpret as "missing" as well as skeleton for creating the metdata tsv (sample list, what interval list was use, the interval list's md5, and what GQ is signified by "missing". Also put some util files in a folder under BlahVariantWalkerUtils for now (should get rid of them eventually but nice to have for now) spacing + adding optional to GQ arguments (whoops) rename intervalListPath to intervalListBlob pass thru sample name swap out errors thrown use L for interval list This doesn't have the level of validation that we need, but works for now Ideally the interval list is required to be a picard interval list file md5 interval list concated string wip split xsvs by contig add vet stripping intial changes review vet trim with Laura fix overzealous missing bug laura seal of approval on schema add back call_DP until we are sure evoq doesn't need it write chr dirs on the fly create dirs for chrs w pet and vet dirs inside add sample id to metadata semantics for sample id move position and sample into main method for easier access add sample id mapping and use it add enum for chr index use longs for the chr addition add array schema and enum add bool for array update array options with sample id and chr adjustment wip to remove chr separation new sample directory structure let the rename begin fixup on walker for arrays more renames better comments fixup on ingest walker * unrelated conflict--maybe merge mistake? * cleanup * swap method for indexed alleles * add genome specific VET creation * move mode enum into common code * wip on adding enums as params
kcibul
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Jan 29, 2021
* initial vet creation class * initial variant walker for jg * initial pet creation class add pet creation to walker update vet schema add headers enum and method to pet creation add xsv creation to loop update vet fix extra delim bug and show non-ref placeholder Also fixed `[.....]` strings in the vet and converted a lot of strings to constants plus a couple of TODOs Fix GT String to output index of alleles instead of allele characters fix enum bug add GQ band to drop as an optional param include end base code used to push PET and VET to BQ added ability to pass in what GQ state to interpret as "missing" as well as skeleton for creating the metdata tsv (sample list, what interval list was use, the interval list's md5, and what GQ is signified by "missing". Also put some util files in a folder under BlahVariantWalkerUtils for now (should get rid of them eventually but nice to have for now) spacing + adding optional to GQ arguments (whoops) rename intervalListPath to intervalListBlob pass thru sample name swap out errors thrown use L for interval list This doesn't have the level of validation that we need, but works for now Ideally the interval list is required to be a picard interval list file md5 interval list concated string wip split xsvs by contig add vet stripping intial changes review vet trim with Laura fix overzealous missing bug laura seal of approval on schema add back call_DP until we are sure evoq doesn't need it write chr dirs on the fly create dirs for chrs w pet and vet dirs inside add sample id to metadata semantics for sample id move position and sample into main method for easier access add sample id mapping and use it add enum for chr index use longs for the chr addition add array schema and enum add bool for array update array options with sample id and chr adjustment wip to remove chr separation new sample directory structure let the rename begin fixup on walker for arrays more renames better comments fixup on ingest walker * unrelated conflict--maybe merge mistake? * cleanup * swap method for indexed alleles * add genome specific VET creation * move mode enum into common code * wip on adding enums as params
kcibul
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Jan 29, 2021
* initial vet creation class * initial variant walker for jg * initial pet creation class add pet creation to walker update vet schema add headers enum and method to pet creation add xsv creation to loop update vet fix extra delim bug and show non-ref placeholder Also fixed `[.....]` strings in the vet and converted a lot of strings to constants plus a couple of TODOs Fix GT String to output index of alleles instead of allele characters fix enum bug add GQ band to drop as an optional param include end base code used to push PET and VET to BQ added ability to pass in what GQ state to interpret as "missing" as well as skeleton for creating the metdata tsv (sample list, what interval list was use, the interval list's md5, and what GQ is signified by "missing". Also put some util files in a folder under BlahVariantWalkerUtils for now (should get rid of them eventually but nice to have for now) spacing + adding optional to GQ arguments (whoops) rename intervalListPath to intervalListBlob pass thru sample name swap out errors thrown use L for interval list This doesn't have the level of validation that we need, but works for now Ideally the interval list is required to be a picard interval list file md5 interval list concated string wip split xsvs by contig add vet stripping intial changes review vet trim with Laura fix overzealous missing bug laura seal of approval on schema add back call_DP until we are sure evoq doesn't need it write chr dirs on the fly create dirs for chrs w pet and vet dirs inside add sample id to metadata semantics for sample id move position and sample into main method for easier access add sample id mapping and use it add enum for chr index use longs for the chr addition add array schema and enum add bool for array update array options with sample id and chr adjustment wip to remove chr separation new sample directory structure let the rename begin fixup on walker for arrays more renames better comments fixup on ingest walker * unrelated conflict--maybe merge mistake? * cleanup * swap method for indexed alleles * add genome specific VET creation * move mode enum into common code * wip on adding enums as params
kcibul
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Feb 1, 2021
* initial vet creation class * initial variant walker for jg * initial pet creation class add pet creation to walker update vet schema add headers enum and method to pet creation add xsv creation to loop update vet fix extra delim bug and show non-ref placeholder Also fixed `[.....]` strings in the vet and converted a lot of strings to constants plus a couple of TODOs Fix GT String to output index of alleles instead of allele characters fix enum bug add GQ band to drop as an optional param include end base code used to push PET and VET to BQ added ability to pass in what GQ state to interpret as "missing" as well as skeleton for creating the metdata tsv (sample list, what interval list was use, the interval list's md5, and what GQ is signified by "missing". Also put some util files in a folder under BlahVariantWalkerUtils for now (should get rid of them eventually but nice to have for now) spacing + adding optional to GQ arguments (whoops) rename intervalListPath to intervalListBlob pass thru sample name swap out errors thrown use L for interval list This doesn't have the level of validation that we need, but works for now Ideally the interval list is required to be a picard interval list file md5 interval list concated string wip split xsvs by contig add vet stripping intial changes review vet trim with Laura fix overzealous missing bug laura seal of approval on schema add back call_DP until we are sure evoq doesn't need it write chr dirs on the fly create dirs for chrs w pet and vet dirs inside add sample id to metadata semantics for sample id move position and sample into main method for easier access add sample id mapping and use it add enum for chr index use longs for the chr addition add array schema and enum add bool for array update array options with sample id and chr adjustment wip to remove chr separation new sample directory structure let the rename begin fixup on walker for arrays more renames better comments fixup on ingest walker * unrelated conflict--maybe merge mistake? * cleanup * swap method for indexed alleles * add genome specific VET creation * move mode enum into common code * wip on adding enums as params
kcibul
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Feb 1, 2021
* initial vet creation class * initial variant walker for jg * initial pet creation class add pet creation to walker update vet schema add headers enum and method to pet creation add xsv creation to loop update vet fix extra delim bug and show non-ref placeholder Also fixed `[.....]` strings in the vet and converted a lot of strings to constants plus a couple of TODOs Fix GT String to output index of alleles instead of allele characters fix enum bug add GQ band to drop as an optional param include end base code used to push PET and VET to BQ added ability to pass in what GQ state to interpret as "missing" as well as skeleton for creating the metdata tsv (sample list, what interval list was use, the interval list's md5, and what GQ is signified by "missing". Also put some util files in a folder under BlahVariantWalkerUtils for now (should get rid of them eventually but nice to have for now) spacing + adding optional to GQ arguments (whoops) rename intervalListPath to intervalListBlob pass thru sample name swap out errors thrown use L for interval list This doesn't have the level of validation that we need, but works for now Ideally the interval list is required to be a picard interval list file md5 interval list concated string wip split xsvs by contig add vet stripping intial changes review vet trim with Laura fix overzealous missing bug laura seal of approval on schema add back call_DP until we are sure evoq doesn't need it write chr dirs on the fly create dirs for chrs w pet and vet dirs inside add sample id to metadata semantics for sample id move position and sample into main method for easier access add sample id mapping and use it add enum for chr index use longs for the chr addition add array schema and enum add bool for array update array options with sample id and chr adjustment wip to remove chr separation new sample directory structure let the rename begin fixup on walker for arrays more renames better comments fixup on ingest walker * unrelated conflict--maybe merge mistake? * cleanup * swap method for indexed alleles * add genome specific VET creation * move mode enum into common code * wip on adding enums as params
Marianie-Simeon
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Feb 16, 2021
* initial vet creation class * initial variant walker for jg * initial pet creation class add pet creation to walker update vet schema add headers enum and method to pet creation add xsv creation to loop update vet fix extra delim bug and show non-ref placeholder Also fixed `[.....]` strings in the vet and converted a lot of strings to constants plus a couple of TODOs Fix GT String to output index of alleles instead of allele characters fix enum bug add GQ band to drop as an optional param include end base code used to push PET and VET to BQ added ability to pass in what GQ state to interpret as "missing" as well as skeleton for creating the metdata tsv (sample list, what interval list was use, the interval list's md5, and what GQ is signified by "missing". Also put some util files in a folder under BlahVariantWalkerUtils for now (should get rid of them eventually but nice to have for now) spacing + adding optional to GQ arguments (whoops) rename intervalListPath to intervalListBlob pass thru sample name swap out errors thrown use L for interval list This doesn't have the level of validation that we need, but works for now Ideally the interval list is required to be a picard interval list file md5 interval list concated string wip split xsvs by contig add vet stripping intial changes review vet trim with Laura fix overzealous missing bug laura seal of approval on schema add back call_DP until we are sure evoq doesn't need it write chr dirs on the fly create dirs for chrs w pet and vet dirs inside add sample id to metadata semantics for sample id move position and sample into main method for easier access add sample id mapping and use it add enum for chr index use longs for the chr addition add array schema and enum add bool for array update array options with sample id and chr adjustment wip to remove chr separation new sample directory structure let the rename begin fixup on walker for arrays more renames better comments fixup on ingest walker * unrelated conflict--maybe merge mistake? * cleanup * swap method for indexed alleles * add genome specific VET creation * move mode enum into common code * wip on adding enums as params
Marianie-Simeon
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Feb 16, 2021
* initial vet creation class * initial variant walker for jg * initial pet creation class add pet creation to walker update vet schema add headers enum and method to pet creation add xsv creation to loop update vet fix extra delim bug and show non-ref placeholder Also fixed `[.....]` strings in the vet and converted a lot of strings to constants plus a couple of TODOs Fix GT String to output index of alleles instead of allele characters fix enum bug add GQ band to drop as an optional param include end base code used to push PET and VET to BQ added ability to pass in what GQ state to interpret as "missing" as well as skeleton for creating the metdata tsv (sample list, what interval list was use, the interval list's md5, and what GQ is signified by "missing". Also put some util files in a folder under BlahVariantWalkerUtils for now (should get rid of them eventually but nice to have for now) spacing + adding optional to GQ arguments (whoops) rename intervalListPath to intervalListBlob pass thru sample name swap out errors thrown use L for interval list This doesn't have the level of validation that we need, but works for now Ideally the interval list is required to be a picard interval list file md5 interval list concated string wip split xsvs by contig add vet stripping intial changes review vet trim with Laura fix overzealous missing bug laura seal of approval on schema add back call_DP until we are sure evoq doesn't need it write chr dirs on the fly create dirs for chrs w pet and vet dirs inside add sample id to metadata semantics for sample id move position and sample into main method for easier access add sample id mapping and use it add enum for chr index use longs for the chr addition add array schema and enum add bool for array update array options with sample id and chr adjustment wip to remove chr separation new sample directory structure let the rename begin fixup on walker for arrays more renames better comments fixup on ingest walker * unrelated conflict--maybe merge mistake? * cleanup * swap method for indexed alleles * add genome specific VET creation * move mode enum into common code * wip on adding enums as params
kcibul
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Mar 9, 2021
* initial vet creation class * initial variant walker for jg * initial pet creation class add pet creation to walker update vet schema add headers enum and method to pet creation add xsv creation to loop update vet fix extra delim bug and show non-ref placeholder Also fixed `[.....]` strings in the vet and converted a lot of strings to constants plus a couple of TODOs Fix GT String to output index of alleles instead of allele characters fix enum bug add GQ band to drop as an optional param include end base code used to push PET and VET to BQ added ability to pass in what GQ state to interpret as "missing" as well as skeleton for creating the metdata tsv (sample list, what interval list was use, the interval list's md5, and what GQ is signified by "missing". Also put some util files in a folder under BlahVariantWalkerUtils for now (should get rid of them eventually but nice to have for now) spacing + adding optional to GQ arguments (whoops) rename intervalListPath to intervalListBlob pass thru sample name swap out errors thrown use L for interval list This doesn't have the level of validation that we need, but works for now Ideally the interval list is required to be a picard interval list file md5 interval list concated string wip split xsvs by contig add vet stripping intial changes review vet trim with Laura fix overzealous missing bug laura seal of approval on schema add back call_DP until we are sure evoq doesn't need it write chr dirs on the fly create dirs for chrs w pet and vet dirs inside add sample id to metadata semantics for sample id move position and sample into main method for easier access add sample id mapping and use it add enum for chr index use longs for the chr addition add array schema and enum add bool for array update array options with sample id and chr adjustment wip to remove chr separation new sample directory structure let the rename begin fixup on walker for arrays more renames better comments fixup on ingest walker * unrelated conflict--maybe merge mistake? * cleanup * swap method for indexed alleles * add genome specific VET creation * move mode enum into common code * wip on adding enums as params
kcibul
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Mar 9, 2021
* initial vet creation class * initial variant walker for jg * initial pet creation class add pet creation to walker update vet schema add headers enum and method to pet creation add xsv creation to loop update vet fix extra delim bug and show non-ref placeholder Also fixed `[.....]` strings in the vet and converted a lot of strings to constants plus a couple of TODOs Fix GT String to output index of alleles instead of allele characters fix enum bug add GQ band to drop as an optional param include end base code used to push PET and VET to BQ added ability to pass in what GQ state to interpret as "missing" as well as skeleton for creating the metdata tsv (sample list, what interval list was use, the interval list's md5, and what GQ is signified by "missing". Also put some util files in a folder under BlahVariantWalkerUtils for now (should get rid of them eventually but nice to have for now) spacing + adding optional to GQ arguments (whoops) rename intervalListPath to intervalListBlob pass thru sample name swap out errors thrown use L for interval list This doesn't have the level of validation that we need, but works for now Ideally the interval list is required to be a picard interval list file md5 interval list concated string wip split xsvs by contig add vet stripping intial changes review vet trim with Laura fix overzealous missing bug laura seal of approval on schema add back call_DP until we are sure evoq doesn't need it write chr dirs on the fly create dirs for chrs w pet and vet dirs inside add sample id to metadata semantics for sample id move position and sample into main method for easier access add sample id mapping and use it add enum for chr index use longs for the chr addition add array schema and enum add bool for array update array options with sample id and chr adjustment wip to remove chr separation new sample directory structure let the rename begin fixup on walker for arrays more renames better comments fixup on ingest walker * unrelated conflict--maybe merge mistake? * cleanup * swap method for indexed alleles * add genome specific VET creation * move mode enum into common code * wip on adding enums as params
mmorgantaylor
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Apr 6, 2021
* initial vet creation class * initial variant walker for jg * initial pet creation class add pet creation to walker update vet schema add headers enum and method to pet creation add xsv creation to loop update vet fix extra delim bug and show non-ref placeholder Also fixed `[.....]` strings in the vet and converted a lot of strings to constants plus a couple of TODOs Fix GT String to output index of alleles instead of allele characters fix enum bug add GQ band to drop as an optional param include end base code used to push PET and VET to BQ added ability to pass in what GQ state to interpret as "missing" as well as skeleton for creating the metdata tsv (sample list, what interval list was use, the interval list's md5, and what GQ is signified by "missing". Also put some util files in a folder under BlahVariantWalkerUtils for now (should get rid of them eventually but nice to have for now) spacing + adding optional to GQ arguments (whoops) rename intervalListPath to intervalListBlob pass thru sample name swap out errors thrown use L for interval list This doesn't have the level of validation that we need, but works for now Ideally the interval list is required to be a picard interval list file md5 interval list concated string wip split xsvs by contig add vet stripping intial changes review vet trim with Laura fix overzealous missing bug laura seal of approval on schema add back call_DP until we are sure evoq doesn't need it write chr dirs on the fly create dirs for chrs w pet and vet dirs inside add sample id to metadata semantics for sample id move position and sample into main method for easier access add sample id mapping and use it add enum for chr index use longs for the chr addition add array schema and enum add bool for array update array options with sample id and chr adjustment wip to remove chr separation new sample directory structure let the rename begin fixup on walker for arrays more renames better comments fixup on ingest walker * unrelated conflict--maybe merge mistake? * cleanup * swap method for indexed alleles * add genome specific VET creation * move mode enum into common code * wip on adding enums as params
mmorgantaylor
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Apr 6, 2021
* initial vet creation class * initial variant walker for jg * initial pet creation class add pet creation to walker update vet schema add headers enum and method to pet creation add xsv creation to loop update vet fix extra delim bug and show non-ref placeholder Also fixed `[.....]` strings in the vet and converted a lot of strings to constants plus a couple of TODOs Fix GT String to output index of alleles instead of allele characters fix enum bug add GQ band to drop as an optional param include end base code used to push PET and VET to BQ added ability to pass in what GQ state to interpret as "missing" as well as skeleton for creating the metdata tsv (sample list, what interval list was use, the interval list's md5, and what GQ is signified by "missing". Also put some util files in a folder under BlahVariantWalkerUtils for now (should get rid of them eventually but nice to have for now) spacing + adding optional to GQ arguments (whoops) rename intervalListPath to intervalListBlob pass thru sample name swap out errors thrown use L for interval list This doesn't have the level of validation that we need, but works for now Ideally the interval list is required to be a picard interval list file md5 interval list concated string wip split xsvs by contig add vet stripping intial changes review vet trim with Laura fix overzealous missing bug laura seal of approval on schema add back call_DP until we are sure evoq doesn't need it write chr dirs on the fly create dirs for chrs w pet and vet dirs inside add sample id to metadata semantics for sample id move position and sample into main method for easier access add sample id mapping and use it add enum for chr index use longs for the chr addition add array schema and enum add bool for array update array options with sample id and chr adjustment wip to remove chr separation new sample directory structure let the rename begin fixup on walker for arrays more renames better comments fixup on ingest walker * unrelated conflict--maybe merge mistake? * cleanup * swap method for indexed alleles * add genome specific VET creation * move mode enum into common code * wip on adding enums as params
mmorgantaylor
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Apr 6, 2021
* initial vet creation class * initial variant walker for jg * initial pet creation class add pet creation to walker update vet schema add headers enum and method to pet creation add xsv creation to loop update vet fix extra delim bug and show non-ref placeholder Also fixed `[.....]` strings in the vet and converted a lot of strings to constants plus a couple of TODOs Fix GT String to output index of alleles instead of allele characters fix enum bug add GQ band to drop as an optional param include end base code used to push PET and VET to BQ added ability to pass in what GQ state to interpret as "missing" as well as skeleton for creating the metdata tsv (sample list, what interval list was use, the interval list's md5, and what GQ is signified by "missing". Also put some util files in a folder under BlahVariantWalkerUtils for now (should get rid of them eventually but nice to have for now) spacing + adding optional to GQ arguments (whoops) rename intervalListPath to intervalListBlob pass thru sample name swap out errors thrown use L for interval list This doesn't have the level of validation that we need, but works for now Ideally the interval list is required to be a picard interval list file md5 interval list concated string wip split xsvs by contig add vet stripping intial changes review vet trim with Laura fix overzealous missing bug laura seal of approval on schema add back call_DP until we are sure evoq doesn't need it write chr dirs on the fly create dirs for chrs w pet and vet dirs inside add sample id to metadata semantics for sample id move position and sample into main method for easier access add sample id mapping and use it add enum for chr index use longs for the chr addition add array schema and enum add bool for array update array options with sample id and chr adjustment wip to remove chr separation new sample directory structure let the rename begin fixup on walker for arrays more renames better comments fixup on ingest walker * unrelated conflict--maybe merge mistake? * cleanup * swap method for indexed alleles * add genome specific VET creation * move mode enum into common code * wip on adding enums as params
mmorgantaylor
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Apr 6, 2021
* initial vet creation class * initial variant walker for jg * initial pet creation class add pet creation to walker update vet schema add headers enum and method to pet creation add xsv creation to loop update vet fix extra delim bug and show non-ref placeholder Also fixed `[.....]` strings in the vet and converted a lot of strings to constants plus a couple of TODOs Fix GT String to output index of alleles instead of allele characters fix enum bug add GQ band to drop as an optional param include end base code used to push PET and VET to BQ added ability to pass in what GQ state to interpret as "missing" as well as skeleton for creating the metdata tsv (sample list, what interval list was use, the interval list's md5, and what GQ is signified by "missing". Also put some util files in a folder under BlahVariantWalkerUtils for now (should get rid of them eventually but nice to have for now) spacing + adding optional to GQ arguments (whoops) rename intervalListPath to intervalListBlob pass thru sample name swap out errors thrown use L for interval list This doesn't have the level of validation that we need, but works for now Ideally the interval list is required to be a picard interval list file md5 interval list concated string wip split xsvs by contig add vet stripping intial changes review vet trim with Laura fix overzealous missing bug laura seal of approval on schema add back call_DP until we are sure evoq doesn't need it write chr dirs on the fly create dirs for chrs w pet and vet dirs inside add sample id to metadata semantics for sample id move position and sample into main method for easier access add sample id mapping and use it add enum for chr index use longs for the chr addition add array schema and enum add bool for array update array options with sample id and chr adjustment wip to remove chr separation new sample directory structure let the rename begin fixup on walker for arrays more renames better comments fixup on ingest walker * unrelated conflict--maybe merge mistake? * cleanup * swap method for indexed alleles * add genome specific VET creation * move mode enum into common code * wip on adding enums as params
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Pr to merge my forked branch into Andrea's gatk branch!