Updated other IntelliJ IDEA warnings in GATKBAMIndex.
Updated example .cram files to match versions generated by current GATK/HTSJDK.
Bumped HTSJDK and Picard to 1.139 releases.
Added support for using `-SNAPSHOT` of HTSJDK in the future.
Previous version of OverclippedReadFilter would only filter a read if both ends of a read had a soft-clipped block.
This adds a boolean option to relax that requirement, and only require 1 soft-clipped block, while also filtering on read length - softclipped length
CRAM now requires .bai index, just like BAM.
Test updates:
- Updated existing MD5s, as TLEN has changed.
- Tests multiple contigs.
- Tests several intervals per contig.
- Tests when `.cram.bai` is missing, even when `.cram.crai` is present.
Updated gatk docs for CRAM support, including:
- Arguments that work for both BAM and CRAM listed as such.
- Arguments that don't work for CRAM either explicitly say "BAM" or "doesn't work for CRAM".
- Instructions on how to recreate a `.cram.bai` using cramtools.
Cleaned up IntelliJ IDEA warnings regarding `Arrays.asList()` -> `Collections.singletonList()`.
-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.
The GATK command line header keys were being repeated in the VCF and
subsequently lost to a single key value by HTSJDK. This resolves
the issue by appending the name of the walker after the text
"GATKCommandLine" and a number after that if the same walker was
used more than once in the form: GATKCommandLine.(walker name) for
the first occurrence of the walker, and GATKCommandLine.(walker name).#
where # is the number of the occurrence of the walker (e.g.
GATKCommandLine.SomeWalker.2 for the second occurrence of SomeWalker).
Integration test added to EngineFeaturesIntegrationTest to verify
two runs of same walker follow expected form.
Resolves#909
See also: HTSJDK #43
* The value of this element (default true) determines whether Queue will explicitly run this walker over unmapped reads
* This patch fixes a runtime error when FindCoveredIntervals was used with Queue
* PT 81777160
* TextCigarCodec.decode() is now static, and the getSingleton() method is gone
* MergingSamRecordIterator now wants a Collection<SamReader> rather than Collection<SAMFileReader> in the constructor
* SeekableBufferedStream now correctly reads the requested number of bytes, removed workaround in GATKBAMIndex
-- Active Region Traversal was using per sample limits on the number of reads that were too low, especially now that we are running one sample at a time. This caused issues with high confidence variants being dropped in high coverage data.
-- HaplotypeCallerGVCFIntegrationTest PL/annotation changes due to using more reads in those tests
-- Removed a CountReadsInActiveRegionsIntegrationTest test for excessive coverage because the read coverage no longer goes over the limits in ART
Reading the multiple GATKText files as a single stream, especially with new top level target executable jar files pointing to a lib folder.
Don't dirty the build with a new GATKText.properties if input files are unmodified.
Stop warning on undocumented abstract classes.
Fixed ClassNotFoundException/NoClassDefFoundError by fixing ResourceBundleExtractorDoclet artifact.
Excluding Exceptions from documentation.
Removed custom log4j dependency from ResourceBundleExtractorDoclet.
Stop generating the dependency reduced pom during shade.
Stop regenerating gsalib when the files are already up to date.
Disabled mvn site generation from external-example.
remove final keyword before refMap and altMap, constructHaplotype() changes their values
return ArtificialHaplotype from constructHaplotype instaed of passing as an argument
Add logic so arraycopy does not throw an IndexOutOfBoundsException, add test for a long insert
Changed tests and scripts to use gatkdir full path instead of relative testdata/qscripts symbolic links.
Although symlinks not created, left the symlink deletion script execution with a comment about future removal.
Re-enabled example UG pipeline queue test.
Replaced all hardcoded strings of {public,private}/testdata with BaseTest variables.
Refactored temp list creation method from ListFileUtilsUnitTest to BaseTest.createTempListFile.
Removed list files with hardcoded paths, now using createTempListFile instead with private test dir variable.
Geraldine Van der Auwera
Ron Levine
meganshand
Mark Fleharty
Chris Norman
Khalid Shakir
Yossi Farjoun
Jacob Silterra
Eric Banks
David Roazen
Alex Baumann
Phillip Dexheimer
seru71
Joel Thibault
Ryan Poplin
Ron Levine