25d943f706
Merge branch 'master' of ssh://chartl@ni.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-01 10:32:11 -05:00
e8528bc526
updating HaplotypeCaller integration tests
2012-02-01 09:43:19 -05:00
dc23265640
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-01 09:22:43 -05:00
579627568e
Limit to 3 ALT alleles
2012-01-31 23:39:39 -05:00
08c7c07f25
Added the option of not compressing read names to ReduceReads
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* When scatter/gathering, name compression cannot guarantee uniqueness. If uniqueness is important, it is recommended to turn compression off for scatter/gathering ReduceReads.
2012-01-31 17:14:57 -05:00
056b24ccd6
Resolving merge conflicts with LocusIteratorByState
2012-01-31 16:13:32 -05:00
febc634557
Changing PileupElement's isSoftClipped to isNextToSoftClip since soft clipped bases aren't actually added to pileups, oops. Removing the intrinsic clustered variants filter from the HaplotypeCaller
2012-01-31 16:06:14 -05:00
7f70612beb
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-31 11:59:25 -05:00
a630db1703
Oops...HierarchicalMicroScheduler was transforming any exception from the walker level into a ReviewedStingException.
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Thanks to Ryan for pointing this out.
2012-01-31 11:58:21 -05:00
a7f5d26326
No more synthetic reads starting/ending with deletions
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bug reported by Kristian Cibulskis that we were generating filtered data synthetic reads with leading deletions. Added integration test.
2012-01-31 11:41:36 -05:00
2f2f039c37
Better flow for byNegTrainingFraction
2012-01-31 10:49:46 -05:00
d8a4d78854
Bugfix for exceptions with unknown source whose error was not being shown in tableau
2012-01-31 10:49:06 -05:00
faba3dd530
Merge branch 'master' of ssh://chartl@ni.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-31 10:25:29 -05:00
17dbe9a95d
A few cleanups in the LocusIteratorByState
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* No more N's in the extended event pileups
* Only add to the pileup MQ0 counter if the read actually goes into the pileup
2012-01-31 09:40:51 -05:00
e7ace8efc4
Fix NullPointerException caused in cases with too many ALT alleles
2012-01-30 21:00:16 -05:00
f9162ea705
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-30 19:45:19 -05:00
abb91cf26b
Increasing the size of the active regions that are produced by the active probability integrator, more context is needed to call more complex events
2012-01-30 15:36:12 -05:00
d5d4fa8a88
Fixed discordance bug reported by Brad Chapman
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discordance now reports discordance between genotypes as well (just like concordance)
2012-01-30 09:50:45 -05:00
f1e07f169e
Only apply filters if there are filters to apply
2012-01-30 02:22:13 -05:00
d1aa5204d7
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-29 23:39:34 -05:00
3186f0f1b0
Try more memory and fewer ALT alleles so that we don't run out of memory
2012-01-29 23:38:32 -05:00
3164c8dee5
S3 upload now directly creates the XML report in memory and puts that in S3
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-- This is a partial fix for the problem with uploading S3 logs reported by Mauricio. There the problem is that the java.io.tmpdir is not accessible (network just hangs). Because of that the s3 upload fails because the underlying system uses tmpdir for caching, etc. As far as I can tell there's no way around this bug -- you cannot overload the java.io.tmpdir programmatically and even if I could what value would we use? The only solution seems to me is to detect that tmpdir is hanging (how?!) and fail with a meaningful error.
2012-01-29 15:14:58 -05:00
0e17cbbce9
Merged bug fix from Stable into Unstable
2012-01-27 16:03:16 -05:00
a9671b73ca
Fix to permit proper handling of mapping qualities between 128 to 255 (which get converted to byte values of -128 to -1)
2012-01-27 16:01:30 -05:00
f7ac1f4a69
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-27 15:12:55 -05:00
fc08235ff3
Bug fix in active region traversal, locusView.getNext() skips over pileups with zero coverage but still need to count them in the active probability integrator
2012-01-27 15:12:37 -05:00
052a4bdb9c
Turning off PHONE HOME option in the MDCP
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* MDCP is for internal use and there is no need to report to the Amazon cloud.
* Reporting to ASW_S3 is not allowing jobs to finish, this is probably a bug.
2012-01-27 11:13:30 -05:00
f8f2152f9c
fixing ReduceReads MD5s
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now that we're using OP instead of OS.
2012-01-27 10:53:24 -05:00
0f2e8400b5
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-27 10:12:50 -05:00
ec9920b04f
Updating the SAM TAG for Original Alignment Start to "OP"
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per Mark's recommendation to reuse the Indel Realigner tag that made it to the SAM spec. The Alignment end tag is still "OE" as there is no official tag to reuse.
2012-01-27 08:51:39 -05:00
13d1626f51
Minor improvements in ref QC walker. Unfortunately this doesn't actually catch Chris's error
2012-01-27 08:24:22 -05:00
cb04c0bf11
Removing javaassist 3.7, lucene library dependancies
2012-01-27 08:24:22 -05:00
2a565ebf90
embarrassing fix-up, thanks Khalid.
2012-01-26 19:58:42 -05:00
0de6aca29b
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-26 18:26:41 -05:00
d54e237671
Take advantage of Eric's fix for multiAllelic AC calculation, and also add fix to have the original allele's INFO field be passed through for batch merging
2012-01-26 18:25:30 -05:00
246e085ec9
Unit tests for GATKSAMRecord class
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* new unit tests for the alignment shift properties of reduce reads
* moved unit tests from ReadUtils that were actually testing GATKSAMRecord, not any of the ReadUtils to it.
* cleaned up ReadUtilsUnitTest
2012-01-26 17:06:36 -05:00
0d4027104f
Reduced reads are now aware of their original alignments
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* Added annotations for reads that had been soft clipped prior to being reduced so that we can later recuperate their original alignments (start and end).
* Tags keep the alignment shifts, not real alignment, for better compression
* Tags are defined in the GATKSAMRecord
* GATKSAMRecord has new functionality to retrieve original alignment start of all reads (trimmed or not) -- getOriginalAlignmentStart() and getOriginalAligmentEnd()
* Updated ReduceReads MD5s accordingly
2012-01-26 17:06:36 -05:00
07f72516ae
Unsupported platform should be a user error
2012-01-26 16:14:25 -05:00
cdff23269d
HaplotypeCaller now uses insertions and softclipped bases as possible triggers. LocusIteratorByState tags pileup elements with the required info to make this calculation efficient. The days of the extended event pileup are coming to a close.
2012-01-26 15:56:33 -05:00
44c3a41f67
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-26 13:25:33 -05:00
dbe9eb70fe
Updating HC integration tests after merge
2012-01-26 13:25:22 -05:00
673ceadd11
While this fix worked for the evaluator module, it could potentially have bad effects in the phasing walkers. Special-case nocalls in the PhasingEvaluator and return AllelePair to previous state.
2012-01-26 13:06:36 -05:00
9c6fda7e15
Yup. I was right.
2012-01-26 12:54:11 -05:00
bd27f3bc9b
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-26 12:52:16 -05:00
67c89cadad
Fixes for pool caller to match UG outputs at certain sites: implement min base qual/min mapping qual read filter so those reads are filtered from pileups, and implemented filter for sites that have a too large a fraction of deletions
2012-01-26 12:52:00 -05:00
7d059540a4
Allow segments of genome to be excluded in generating a reference panel. Occasionally targets would contain no variation (typically, in the middle of the centromere), which beagle doesn't particularly like, and errors out rather than producing empty output files. The best way to deal with these is to just exclude the regions on a second-pass, and the remaining bits will be gathered with no additional work.
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AllelePair is being mean and not telling me what genotype it sees when it finds a non-diploid genotype, but i suspect it's a no-call (".") rather than a no call ("./.").
2012-01-26 12:43:52 -05:00
9d4b84f6bd
Merge branch 'master' of ssh://chartl@ni.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-26 12:38:24 -05:00
25532bdc37
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-26 11:43:32 -05:00
390d493049
Updating ActiveRegionWalker interface to output a probability of active status instead of a boolean. Integrator runs a band-pass filter over this probability to produce actual active regions. First version of HaplotypeCaller which decides for itself where to trigger and assembles those regions.
2012-01-26 11:37:08 -05:00
9a63a9ae3c
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-26 00:38:25 -05:00
Christopher Hartl
Ryan Poplin
Menachem Fromer
Mauricio Carneiro
Matt Hanna
Mark DePristo
Eric Banks
Guillermo del Angel