c8cda209b5
Make intersection easy to change
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Write each client's output to a different file
2012-06-12 15:46:34 -04:00
1da3e43679
Wow, apparently it's way, way less efficient to iterate over Java Lists than native arrays. With this change and the bit fiddling, Ryan's 10-day test case now runs in 1 day. More to come.
2012-06-12 13:32:56 -04:00
a96c5da884
Oops, forgot to push the unit tests
2012-06-12 11:38:30 -04:00
a057cf31b3
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-06-12 11:02:50 -04:00
fec0bd5e11
Fixing UG argument docs
2012-06-12 09:46:16 -04:00
a4defdfb29
Adding a GT header line to SomaticIndelDetector output
2012-06-12 09:39:17 -04:00
891ce51908
Refactoring of BQSRv2 to use longs (and standard bit fiddling techniques) instead of Java BitSets for performance improvements.
2012-06-12 09:19:36 -04:00
0c98c34f5f
Fixing bugs caught by Eric
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* if a read starts with insertion, and is part of a read that overlaps both the consensus and the variant region, and the insertion is the first base of this read. Don't try to remove it.
* keep the last header element in a variant region to prevent adjacent reads starting with insertions from breaking when trying to remove the header element before the insertion.
2012-06-11 17:32:49 -04:00
e0fbffac3a
Fixing bugs caught by Eric
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* if a read starts with insertion, and is part of a read that overlaps both the consensus and the variant region, and the insertion is the first base of this read. Don't try to remove it.
*
2012-06-11 17:32:49 -04:00
ff5749599d
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-06-11 15:46:17 -04:00
fea625632f
Don't use asList because it maintains an iterator to the original list and then the result can't be used to create a new one
2012-06-11 15:45:58 -04:00
41ef22fe7c
Re-enabling BQSR integration tests
2012-06-11 15:44:55 -04:00
e4d371dc80
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-06-11 10:38:50 -04:00
683d4b508e
Bug fix in fragment utils: the read name wasn't being set in the merged read. Misc minor updates to the HaplotypeCaller.
2012-06-11 10:38:35 -04:00
4aad7e23ef
New ReduceReads v2 with unclipped variant regions and soft-clipped bases
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* Re-wrote the sliding window approach to allow the variant region not to clip the reads that overlap it.
* Updated consensus to include only reads that were not passed on by the variant region, header counts are updated on the fly to avoid recompute
* Added soft clipped bases to ReduceReads analysis by unclipping high quality soft-clips then re-clipping after reduce reads
* Updated all integration tests
2012-06-08 14:58:31 -04:00
edf08ca928
Updates to ReduceReads
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* Turn off the post-downsampler by default until new implementation.
* optimized read clipping in consensus regions -- only clip once instead of every time the window slides.
* extracted HeaderElement into it's own class.
* moved RFA to archive
* unified the context size of indels and mismatches
2012-06-08 14:57:34 -04:00
afa9b2718a
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-06-08 13:54:48 -04:00
92280b4068
BQSR optimization: cache the BitSetUtils.bitSetFrom() calls since they are called over and over again with the same values. Another 10% reduction in runtime.
2012-06-08 13:54:37 -04:00
898a0e6161
Minor optimizations
2012-06-08 12:07:58 -04:00
0a37e19998
Bug fix in VQSR so that the VCF index will be created for the recalFile.
2012-06-08 11:51:28 -04:00
d463ab2cbf
BQSR optimization: String manipulation is extremely expensive in Java (accounts for 8% of BQSR runtime). Instead use byte[] and StringBuilder when possible.
2012-06-08 10:42:42 -04:00
2bd48a7351
Bad comments made it into the previous commit
2012-06-07 23:12:56 -04:00
31c3a6be48
BQSR optimization: getRequiredCovariates() and getOptionalCovariates() were creating a new List every time they were being called, and unfortunately getRequiredCovariates().size() is used as the stop condition in for-loops throughout the code. Just maintaining the original list of covariates results in a 15% reduction in runtime for BQSR.
2012-06-07 20:04:10 -04:00
0fb9179f76
BQSR optimization: don't clone the original quals for each read, we can just overwrite the original array
2012-06-07 19:41:03 -04:00
32e4fe5c87
Enable zero-sample testing
2012-06-07 14:43:13 -04:00
fe9dc0cc3f
Explicitly set intervals in new test
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mem limit 4g
2012-06-07 14:43:13 -04:00
0ac4ba9ad3
unintended change crept in
2012-06-07 10:59:04 -04:00
d449f169d3
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-06-07 10:56:55 -04:00
0b4281fdd0
misc minor update to HC debug output for when there are a lot of samples
2012-06-07 10:56:41 -04:00
bad50a1b05
Fix docs
2012-06-06 22:45:38 -04:00
b093ba9dcc
Stabilized NGSPlatform code: don't assume all reads have read groups (e.g. artificial SAM records)
2012-06-06 15:17:30 -04:00
54f682a99c
Unify to NGSPlatform framework. TechnologyComposition annotation now generalizes to Illumina and not just SLX.
2012-06-06 11:44:37 -04:00
dd46d843fb
IR should skip Ion reads just like it does with 454 reads; Tim has confirmed that official platform name for Ion.
2012-06-06 11:04:55 -04:00
b6a7c3f780
Merged bug fix from Stable into Unstable
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Resolved merge conflict
Conflicts:
public/java/test/org/broadinstitute/sting/BaseTest.java
2012-06-05 17:44:44 -04:00
3b2fab9a37
Update stable for shptmp -> hptmp migration
2012-06-05 17:38:06 -04:00
2cbd6e5f90
Merged bug fix from Stable into Unstable
2012-06-05 15:58:23 -04:00
ce4dc2128d
Adding minor clarification to -mbq argument documentation
2012-06-05 15:17:56 -04:00
e02ec8c8b6
Don't update the record ID unless we are actually going to emit the record
2012-06-04 14:58:50 -04:00
8405156ae1
Refactored VariantsToTable so that 1) genotype-level fields can be specified (stabilized and supported code) and 2) the --moltenize argument could be supported to produce molten output of the data. Added tests that cover these capabilities.
2012-06-04 14:28:32 -04:00
f11e7ebc3a
Fixing the previous fix related to clipping. Adding extra reference padding in the HaplotypeCaller to get those larger alleles during GGA.
2012-06-04 12:49:36 -04:00
320956ee4b
Bug fix in clipping function in ReadUtils for when the read ends at exactly the clipping boundary. Bug fixes in HaplotypeCaller GGA mode for when Smith-Waterman produces a different allele than what was given in the input alleles VCF. GGA mode now works with multiallelic records. Adding min pruning factor argument which is combined with the pruning factor that is determined dynamically by the coverage.
2012-06-04 10:55:36 -04:00
7a54baf08c
Merged bug fix from Stable into Unstable
2012-06-03 08:42:08 -04:00
47df7bbc14
Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable
2012-06-03 08:38:54 -04:00
2ddbdee3bc
Fixed broken VariantEval stratifications VariantType and IndelSize - integration tests to follow
2012-06-03 08:38:38 -04:00
12a8c54f9a
Fixing VCF header for filter elements (thanks Eric)
2012-06-01 15:45:15 -04:00
3b20b4615d
ant fasttest: for when you just can't wait
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Cuts major corners for speed. Tests start in SECONDS instead of minutes.
SIGNIFICANT limitations (see below!)
Usage: ant fasttest -Dsingle=TestClass
The idea is that you do a regular "ant test -Dsingle=TestClass" (or "ant committests")
FIRST, then do "ant fasttest -Dsingle=TestClass" for all subsequent runs until
satisfied.
LIMITATIONS:
-REQUIRES that a full test build has already been done (using one of the
test targets like committests, or a manual "ant test.compile").
-Java only
-Single test class only
-No contracts
-Build jars in dist/ not updated, only classes in build/
-Version number output at runtime may be incorrect
2012-06-01 15:17:18 -04:00
2e3af1a739
Enable contracts for the release jar tests (whoops...)
2012-06-01 13:08:46 -04:00
fdf607c3a9
One-off walker but techdev may find it useful and expand on it: given a BAM, output series of intervals to file (as interval_list [default] or BED [if -bed used]) where there is coverage. Additionally, print out to stdout at the end total covered bases and total covered bases including soft-clips
2012-05-31 20:47:37 -04:00
3a15ba2102
Malformed VCF headers should be User Errors
2012-05-31 16:05:53 -04:00
d1822c926c
Temporary fake release directories for Bamboo testing purposes
2012-05-31 16:04:07 -04:00
Joel Thibault
Eric Banks
Mauricio Carneiro
Ryan Poplin
David Roazen
Guillermo del Angel