-We now pull htsjdk and picard from maven central.
-Updated the GATK codebase as necessary to adapt to changes in the Feature
interface.
-Since VCFHeader now requires that all header lines have unique keys, uniquified
the keys of GVCFBlock header lines by including the min/max GQ in the key.
Updated MD5s accordingly.
-Other MD5s changed as a result of an htsjdk fix to eliminate "-0" in VCF output.
* Removed unused annotations (CCC and HWP)
* Renamed one of the two GC annotations to "IGC" (for Interval GC)
* Revved picard & htsjdk (GATK constants are now removed from htsjdk)
* PT 82046038
* This argument forces GATK to always write every record in the VCF format field, even if some records at the end are missing and could be removed
* Revved htsjdk and picard
* PT 70993484
ValidationStringency was moved from htsjdk.samtools.SAMFileReader to htsjdk.samtools
samtools find BAM index file method was also moved (and made public!)
To reduce merge conflicts, this commit modifies contents of files, while file renamings are in previous commit.
See previous commit message for list of changes.
-Only works with single-sample vcfs
-As with bams, the user must provide a file mapping the absolute path to
each vcf whose samples are to be renamed to the new sample name for that
vcf. The argument is the same as for bams: --sample_rename_mapping_file,
and the mapping file may contain a mix of bam and vcf files should the
user wish.
-It's an error to attempt to remap the sample names of a multi-sample
or sites-only vcf
-Implemented at the codec level at the instant the vcf header is first
read in to minimize the chances of downstream code examining vcf
headers/records before renaming occurs.
-Integration tests are in sting, unit tests are in picard
-Rev picard et. al. to 1.111.1902
- SamPairUtils migrated in Picard r1737
- Revert IndelRealigner changes made in commit 4f4b85
-- Those changes were based on Picard revision 1722 to net/sf/picard/sam/SamPairUtil.java
-- Picard revision 1723 reverts these changes, so we also revert to match
1. Enable on-the-fly indexing for vcf.gz.
2. Handle on-the-fly indexing where file to be indexed is not a regular file, thus index should not be created.
3. Add method setProgressLogger to all SAMFileWriter implementations.
4. Revved picard to 1.109.1722
5. IndelRealigner md5s change because the MC tag is added to records now.
Fixed up and signed off by ebanks.
New properties to disable regenerating example resources artifact when each parallel test runs under packagetest.
Moved collection of packagetest parameters from shell scripts into maven profiles.
Fixed necessity of test-utils jar by removing incorrect dependenciesToScan element during packagetests.
When building picard libraries, run clean first.
Fixed tools jar dependency in picard pom.
Integration tests properly use the ant-bridge.sh test.debug.port variable, like unit tests.
Ron Levine
Louis Bergelson
David Roazen
Khalid Shakir
Phillip Dexheimer
Laura Gauthier
Joel Thibault
Alec Wysoker