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()`.
When using CatVariants, VCF files were being sorted solely on the base
pair position of the first record, ignoring the chromosome. This can
become problematic when merging files from different chromosomes,
espeically if you have multiple VCFs per chromosome.
As an example, assume the following 3 lines are all in separate files:
1 10
1 100
2 20
The merged VCF from CatVariants (without -assumeSorted) would read:
1 10
2 20
1 100
This has the potential to break tools that expect chromosomes to be
contiguous within a VCF file.
This commit changes the comparator from one of Pair<Integer, File> to
one of Pair<VariantContext, File>. We construct a
VariantContextComparator from the provided reference, which will sort
the first record by chromosome and position properly. Additionally, if
-assumeSorted is given, we simply use a null VariantContext as the first
record, which will all be equal (as all will be null)
-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.
Exclude MQ0BySample
Move SD and TRA to new StandardUGAnnotation interface
There is now annotation interface (StandardUGAnnotation) holding annots that are standard in UG but should't be used as they are now with HC. This allows us to not have to exclude these annotations explicitly in HC, but still be able to use them for development purposes.
Fairly minor if plentiful fixes to various gatkdocs. Merging this without formal review since all tests pass, the gatkdocs build, and no one really wants to review corrections to grammar, typos and layout for 120+ documents. Review will be done by users in production ;-)
Build a ReferenceContext in ActiveRegionWalkers to pass in to annotation engine so we can call the TandemRepeatAnnotator from M2
Make TandemRepeatAnnotator default annotation for M2.
Setup (but don't use yet) HC-style contamination downsampling.
New HC integration test with TandemRepeatAnnotator
- ASEReadCounter (public tool) replce Tuuli's script to produce the input to Manny's tool.
It count the number of reads that support the ref allele and the alt allele, filtereing low qual reads and bases and keep only properPaired reads
- ASECaller (private tool) take both RNA and DNA, and produce ontingencyTables ** still under development **
minor changes in other tools:
- update RNA HC variant calling scala script
- expose FS method pValueForContingencyTable to be able to call it from ASEcaller
In ASEReadCounter:
- allow different option to deal with overlaping read from the same fragment
- add option to ignore or include indels in the pileups
- add option to disabled DuplicateRead
add ASEReadCounterIntegrationTest.java and files for the test
Geraldine Van der Auwera
Ami Levy Moonshine
Ron Levine
Bertrand Haas
Khalid Shakir
David Benjamin
Louis Bergelson
Joseph White
Eric Banks
John Wallace
David Roazen
Ami Levy-Moonshine
ldgauthier
Phillip Dexheimer