b85ded8389
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-30 10:11:48 -04:00
650ff29e62
oops, I meant to use binary OR here.
2012-08-30 10:11:29 -04:00
57d997f06f
Fixing bug from when FragmentUtils merging function moved over to the soft clipped start instead of the unclipped start
2012-08-30 10:10:43 -04:00
f9bab37015
Merged bug fix from Stable into Unstable
2012-08-30 09:21:24 -04:00
eb63221875
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2012-08-30 09:19:35 -04:00
81d5eca975
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-30 09:10:56 -04:00
35baf0b155
This along with Mauricio's previous commit (thanks!) fixes GSA-522. There are no longer any modifications to reads in the map calls of ActiveRegion walkers. Added the bam which identified this error as a new integration test.
2012-08-30 09:07:36 -04:00
1acf0f0b2c
Fixing bug in fasta .fai generation: trim the contig names to the first whitespace if one appears. We now generate indexes identical to samtools.
2012-08-29 22:36:27 -04:00
4d38befe86
Merged bug fix from Stable into Unstable
2012-08-29 15:13:56 -04:00
150a969279
Be careful with String manipulation when constructing alleles in SomaticIndelDetector
2012-08-29 15:13:28 -04:00
ce55ba98f4
Don't try to left align indels in unmapped reads (which for some reason can still have CIGARs) because the ref context is null.
2012-08-29 15:01:11 -04:00
4ea38bbfe8
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-29 11:39:30 -04:00
b132a33dac
Delocalized BQSR now BAQs the reads on the fly instead of on input.
2012-08-29 11:39:07 -04:00
69b56e11c8
ReadClipper won't modify the original read
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Reverting back to the original implementation, but now including write N's and write Q0's due to walkers that look at the same read multiple times in different reference windows
2012-08-29 11:33:19 -04:00
e12ae65d33
Changing the commenting style in the BQSR
2012-08-29 11:27:45 -04:00
19cc0b373e
Some code review comments for Ryan
2012-08-28 17:06:08 -04:00
f45226f01e
Updated HSPTest expected values to match FS changes in depristo's 3baf52 commit.
2012-08-28 16:34:55 -04:00
6d6ca090c6
RecalDatums now hold doubles so the test for equality needs an epsilon.
2012-08-28 16:00:52 -04:00
18eca3544e
Initial commit of the delocalized BQSR written as a read walker.
2012-08-28 15:24:20 -04:00
e74c527d47
Register the depricated walkers as depricated starting in v2.2 so that users get a helpful error message
2012-08-28 10:19:18 -04:00
67d348a31d
Retiring the alignment walkers and related integration test since we don't want to support them anymore.
2012-08-28 10:16:49 -04:00
0f4acaae1b
Update MD5s with new FS score
2012-08-28 08:06:47 -04:00
4b8d9c3915
Actually load the library necessary to compactPDF
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-- Old version was buggy in that if you didn't load "tools" package in your script it wouldn't compact the resulting PDF! Fixed
2012-08-28 08:06:47 -04:00
2996693c9f
FisherStrand now computed with and without filtering low-qual bases, and least significant pvalue is kept
...
-- Old way (filtering for Q > 17 bases) resulted in biased FS when the site was good but there was a
systematic shift in the QUAL of REF and ALT between strands of the reads (sometimes happens)
-- New way (taking all bases) was consistent with BaseQualRankSum and other tests, but there can be
a lot of low qual reference bases on one strand in some techs (ION/PROTON/PACBIO) because of the
preference for introducing an indel vs. a mismatch.
-- This implementation allows us to have our cake and eat it to by computing both p-values, and
taking the maximum one (i.e., least significant).
-- No integration tests updated yet -- still exploring the consequences of this change
2012-08-28 08:06:47 -04:00
bedcdbdc5f
Fixing merge conflict
2012-08-27 12:16:51 -04:00
3d476487c6
LIBS is totally busted for deletions. Putting a check in AD for bad pileup event bases so that we don't produce busted alleles. We must fix LIBS ASAP.
2012-08-27 12:13:12 -04:00
63a9ae817a
Ensure thread-safety of CachingIndexedFastaSequenceFile
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-- Cosmetic cleanup of ReadReferenceView
-- TraverseReadsNano provides the reference context, since it's thread-safe
-- Cleanup CachingIndexedFastaSequenceFile. Add docs, remove unnecessary setters
-- Expand CachingIndexedFastaSequenceFileUnitTest to test explicitly multi-threaded safety.
2012-08-27 12:11:54 -04:00
e5b1f1c7f4
Add simple main function to unit test so we can run the nano scheduler test from the command line
2012-08-27 12:11:54 -04:00
2d1ea7124b
One less Queue command line requirement: -tempDir now defaults to .queue/tmp.
...
Also moved queueScatterGather to .queue/scatterGather.
2012-08-27 12:04:50 -04:00
68c5142d2d
numThreads > 1 any time you have -nt > 1 silly
2012-08-26 14:36:13 -04:00
faacacd6c0
Increase runtime of nano scheduler tests to 1 min
2012-08-26 08:42:58 -04:00
846e0c11bc
Add TimeOuts to new threading tests, in case there's a underlying deadlock
2012-08-26 08:18:43 -04:00
fde9824765
Optimizations for parallel read walkers
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-- TraversalReadsNano only creates the NanoScheduler once, and shuts it down onTraversalDone
-- Nicer debugging output in NanoScheduler
-- ReadShard has a getBufferSize() method now
2012-08-25 17:21:12 -04:00
5066b14335
Parallel FlagStat
2012-08-25 17:21:12 -04:00
af540888f1
Limited version of parallel read walkers
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-- Currently doesn't support accessing reference or ROD data
-- Parallel versions of PrintReads and CountReads
2012-08-25 17:21:12 -04:00
e060b148e2
Minor cleanup of TraverseReads
2012-08-25 17:21:11 -04:00
275a5e5439
More tests for NanoScheduler
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-- Add more contracts
-- Test in the UnitTest that the reduce is being called in the correct order
2012-08-25 17:21:11 -04:00
6db0988898
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-08-25 15:40:32 -04:00
db2e88c7cb
Fix for badIndelLength() throwing NPE at non-indel sites. Added integration test.
2012-08-25 12:38:23 -07:00
59b5913b54
Merged bug fix from Stable into Unstable
2012-08-25 14:53:22 -04:00
dcc972a557
Usability cleanup for BQSR
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-- I'm seeing a lot of people trying to use BinaryTagCovariate in the community. They really shouldn't do this, so I moved it to private.
-- Throw an exception if its required bintag argument is missing
-- Check explicitly if user is requesting DinucCovariate and tell them that its been retired in favor of ContextCovariate
-- Show the type (Required, Experimental, Standard) of the covariates when running --list
2012-08-25 14:53:00 -04:00
1044ddbc26
Minor improvement in naming of BQSR tests
2012-08-25 14:06:55 -04:00
58ca3f61df
Fix horrible bug in the classification of runs as successes, sting-exceptions, or user-exceptions in analyzeRunReports
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-- Old logic was just busted.
2012-08-25 14:06:55 -04:00
b59948709f
Code improvements re: JIRA GSA-510. Trio class migrated into the Samples package - because the trio structure is so ubiquitously used, it makes sense, I think, to have a class which imposes the structure on the samples. Existing functions which slightly duplicated the getTrios() method look like they have bugs. These functions are now deprecated.
...
A number of functions int he sampleDB looked to be assuming that samples could not share IDs (e.g. sample IDs are unique, so a sample present in two families could not be represented by multiple Sample objects). Added an assertion in the SampleDBBuilder to document/test this assumption.
MVLikelihoodRatio now uses the trio methods from SampleDB.
2012-08-25 08:48:27 -07:00
0996bbd548
Comments for Chris on cleanup
2012-08-24 16:04:58 -04:00
649b82ce85
Merge branch 'nanoScheduler'
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Conflicts:
private/scala/qscript/org/broadinstitute/sting/queue/qscripts/performance/GATKPerformanceOverTime.scala
2012-08-24 15:59:36 -04:00
801b910b9e
GATKPerformanceOverTime is finalized (mark II)
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-- Make BQSR run longer
-- Use Dinuc not context covariates for BQSR v1
2012-08-24 15:57:48 -04:00
62aa0ac77e
GATKPerformanceOverTime is finalized
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-- Update BQSR to run v1 and v2. Use new single read group extracted BAM
-- Bug fixes
2012-08-24 15:57:48 -04:00
3bbdccb0ae
Refactor and cleanup GATKPerformanceOverTime
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-- Use single read group BAM file for BQSR
-- Implement terrible (but clever) hack to support BQSR v1 and v2 in a single Scala class.
2012-08-24 15:57:48 -04:00
9f0eff4c4c
MySQLdb required to run analyzeRunReports, despite my best efforts
2012-08-24 15:57:48 -04:00
Ryan Poplin
Eric Banks
Mauricio Carneiro
Mark DePristo
Khalid Shakir
Christopher Hartl