The ParallelShell job runner will run jobs locally on one node concurrently as specified by the DAG, with the option to limit the maximum number of concurrently running jobs using the flag `maximumNumberOfJobsToRunConcurrently`.
Signed-off-by: Khalid Shakir <kshakir@broadinstitute.org>
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.
This change doesn't affect the performance of the Indel Realigner at all (as per tests).
This is just a request from the Picard side (where further testing is happening).
Make MQ threshold a parameter (compare to M1 by setting to zero)
Add logic for multiple alternate alleles in tumor
Exclude MQ0 normal reads from normal LOD calculation
Fix path errors in Dream_Evaluations.md
Move M2 eval scripts out of walkers package so they run
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()`.
Changed a division by -10.0 to a multiplication by -.1 in QualUtils (typically multiplication is faster than division).
Addresses performance issue #1081.
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)
Takuto Sato
Chris Norman
Ron Levine
Eric Banks
Kate Noblett
Khalid Shakir
Johan Dahlberg
samuelklee
Geraldine Van der Auwera
Samuel Lee
Ami Levy Moonshine
meganshand
ldgauthier
Mark Fleharty
Bertrand Haas
Yossi Farjoun
Jacob Silterra
David Benjamin
Louis Bergelson
vruano
David Roazen
Valentin Ruano Rubio
Joseph White
John Wallace