gatk-3.8

Author	SHA1	Message	Date
delangel	b6bdd61283	a) Fix bug when multi-base reference is homopolymeric when writing a VCF4.0 variant context: computation of number of trailing bases was incorrect and we ended up with incorrect position. b) Updated VCF4WriterTestWalker to take either VCF3 or VCF4 as inputs (this walker can also be used to convert from 3.3 to 4.0). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3711 348d0f76-0448-11de-a6fe-93d51630548a	2010-07-02 15:19:42 +00:00
delangel	3ca2b7374b	Fixes to better deal with the "Type" and "Number" field in the INFO and FORMAT header lines in VCF4.0. We now record these fields and provide appropriate conversions. This is the first version that passes fully the VCF validator. Also, moved the flag indicating VCF4.0 to the VCFWriter constructor. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3669 348d0f76-0448-11de-a6fe-93d51630548a	2010-06-29 16:43:00 +00:00
delangel	ed71e53dd4	1) Initial complete version of VCF4 writer. There are still issues (see below) but at least this version is fully functional. It incorporates getting rid of intermediate VCFRecord so we now operate from VariantContext objects directly to VCF 4.0 output. See VCF4WriterTestWalker for usage example: it just amounts to adding vcfWriter.add(vc,ref.getBases()) in walker. add() method in VCFWriter is polymorphic and can also take a VCFRecord, lthough eventually this should be obsolete. addRecord is still supported so all backward compatibility is maintained. Resulting VCF4.0 are still not perfect, so additional changes are in progress. Specifically: a) INFO codes of length 0 (e.g. HM, DB) are not emitted correctly (they should emit just "HM" but now they emit "HM=1"). b) Genotype values that are specified as Integer in header are ignored in type and are printed out as Doubles. Both issues should be corrected with better header parsing. 2) Check in ability of Beagle to mask an additional percentage of genotype likelihoods (0 by default), for testing purposes. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3664 348d0f76-0448-11de-a6fe-93d51630548a	2010-06-28 23:54:38 +00:00

Author

SHA1

Message

Date

delangel

a) Fix bug when multi-base reference is homopolymeric when writing a VCF4.0 variant context: computation of number of trailing bases was incorrect and we ended up with incorrect position.

b) Updated VCF4WriterTestWalker to take either VCF3 or VCF4 as inputs (this walker can also be used to convert from 3.3 to 4.0).
 


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3711 348d0f76-0448-11de-a6fe-93d51630548a

2010-07-02 15:19:42 +00:00

delangel

3ca2b7374b

Fixes to better deal with the "Type" and "Number" field in the INFO and FORMAT header lines in VCF4.0. We now record these fields and provide appropriate conversions. This is the first version that passes fully the VCF validator.

Also, moved the flag indicating VCF4.0 to the VCFWriter constructor.

 


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3669 348d0f76-0448-11de-a6fe-93d51630548a

2010-06-29 16:43:00 +00:00

delangel

ed71e53dd4

1) Initial complete version of VCF4 writer. There are still issues (see below) but at least this version is fully functional. It incorporates getting rid of intermediate VCFRecord so we now operate from VariantContext objects directly to VCF 4.0 output.

See VCF4WriterTestWalker for usage example: it just amounts to adding
vcfWriter.add(vc,ref.getBases()) in walker.

add() method in VCFWriter is polymorphic and can also take a VCFRecord, lthough eventually this should be obsolete.
addRecord is still supported so all backward compatibility is maintained.

Resulting VCF4.0 are still not perfect, so additional changes are in progress. Specifically:
a) INFO codes of length 0 (e.g. HM, DB) are not emitted correctly (they should emit just "HM" but now they emit "HM=1").
b) Genotype values that are specified as Integer in header are ignored in type and are printed out as Doubles.

Both issues should be corrected with better header parsing.

2) Check in ability of Beagle to mask an additional percentage of genotype likelihoods (0 by default), for testing purposes.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3664 348d0f76-0448-11de-a6fe-93d51630548a

2010-06-28 23:54:38 +00:00

3 Commits (530a320f2876ff2c3a4e21f3f4ce922963c43fed)