a) VCF track name can work again with 3.3 or 4.0 VCF's when specifying -B name,VCF,file. Code will read header and parse automatically the version.
b) Old VCF codec is deprecated. Reader goes now direct from parsing VCF lines into producing VariantContext objects, with no intermediate VCF records. If anyone can't resist the urge to still input files using the old method, a new VCF3Codec is in place with the old code, but it will be eventually deleted.
c) VCF headers and VCF info fields no longer keep track of the version. They are parsed into an internal representation and will be output only in VCF4.0 format.
d) As a consequence, the existing GATK bug where files are produced with VCF4 body but VCF3.3 headers is solved.
e) Several VCF 4.0 writer bugs are now solved.
f) Integration test MD5's are changed, mostly because of corrected VCF4.0 headers and because validation data mostly uses now VCF4.0.
g) Several VCF files in the ValidationData/ directory have been converted to VCF 4.0 format. I kept the old versions, and the new versions have a .vcf4 extension.
Pending issues:
a) We are still not dealing with indels consistently or correctly when representing them. This will be a second part of the changes.
b) The VCF writer doesn't use VCFRecord but it does still use a lot of leftovers like VCFGenotypeEncoding, VCFGenotypeRecord, etc. This needs to be simplified and cleaned.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3813 348d0f76-0448-11de-a6fe-93d51630548a
-Remove in-memory sorting
-Default to name-sorting (although we allow coordinate sorting with the --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe flag).
Cleaner, faster code. Wiki has been updated (including how to use FixMateInformation.jar from Picard). More changes coming soon.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3612 348d0f76-0448-11de-a6fe-93d51630548a
We almost completely support indels. Not yet done with plink stuff.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2926 348d0f76-0448-11de-a6fe-93d51630548a
Also updating other IntervalCleanerIntegrationTest failures that were masked by my first patch.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2440 348d0f76-0448-11de-a6fe-93d51630548a
1) sam-jdk apparently no longer supports custom tags with type int[] values.
2) BAM output for indel cleaner integration test changed in a way that's so subtle it can't be seen after converting the output to .sam.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2439 348d0f76-0448-11de-a6fe-93d51630548a
Also, slightly optimized the cleaner by using readBases (instead of readString) and caching cigar element lengths.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2419 348d0f76-0448-11de-a6fe-93d51630548a
-Bamboo will now run the integration tests once a day, and the normal units tests on each check-in.
-Also added a bunch of unit tests for VariantEval walker
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1555 348d0f76-0448-11de-a6fe-93d51630548a
-I also uncovered a corner case in the cleaner that for some reason was commented out but shouldn't have been. Hooray for unit tests!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1553 348d0f76-0448-11de-a6fe-93d51630548a
rough initial implementation, but should provide enough support so that people can stop
creating SAMFileWriters in reduceInit.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1332 348d0f76-0448-11de-a6fe-93d51630548a
delangel
aaron
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depristo
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