5343f8ba67
Initial version of on-the-fly, lazy loading base quality score recalibration. It isn't completely hooked up yet but I'm committing so Mauricio and Mark can see how I envision it will fit together. Look it over and give any feedback. With the exception of the Solid specific code we are very very close to being able to remove TableRecalibrationWalker from the code base and just replace it with PrintReads -BQSR recal.csv
2012-02-05 13:09:03 -05:00
f94d547e97
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-03 17:14:20 -05:00
894d3340be
Active Region Traversal should use GATKSAMRecords everywhere instead of SAMRecords. misc cleanup.
2012-02-03 17:13:52 -05:00
4a57add6d0
First implementation of DiagnoseTargets
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* calculates and interprets the coverage of a given interval track
* allows to expand intervals by specified number of bases
* classifies targets as CALLABLE, LOW_COVERAGE, EXCESSIVE_COVERAGE and POOR_QUALITY.
* outputs text file for now (testing purposes only), soon to be VCF.
* filters are overly aggressive for now.
2012-02-03 17:12:43 -05:00
3dd6a1f962
Adding some generic sum and average functions to MathUtils
2012-02-03 17:12:43 -05:00
e1d69e4060
make the size of a GenomeLoc int instead of long
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it will never be bigger than an int and it's actually useful to be an int so we can use it as parameters to array/list/hash size creation.
2012-02-03 17:12:42 -05:00
0e44430e47
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-03 13:45:11 -05:00
aa3638ecb3
Merge branch 'master' of ssh://chartl@ni.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-03 13:42:09 -05:00
3abfbcbcf2
Generalized the TDT for multi-allelic events
2012-02-03 12:23:21 -05:00
601e53d633
Fix when specifying preset active regions with -AR argument
2012-02-02 16:34:26 -05:00
0111505ea9
Terrible. Swapping the paternal and sample ids.
2012-02-02 11:41:16 -05:00
1f50f6970b
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-02-02 10:17:13 -05:00
4ed06801a7
Updating HaplotypeCaller's HMM calc to use GOP as a function of the read instead of a function of the haplotype in preparation for IQSR
2012-02-02 10:17:04 -05:00
8adfc79123
Merged bug fix from Stable into Unstable
2012-02-01 16:07:41 -05:00
30b937d2af
Fix bug discovered in FGTP branch in which BlockInputStream returns -1 in cases where some data could be read,
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but not all the data requested by the caller.
2012-02-01 16:06:22 -05:00
45da892ecc
Better exceptions to catch malformed reads
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* throw exceptions in LocusIteratorByState when hitting reads starting or ending with deletions
2012-02-01 11:56:19 -05:00
810996cfca
Introducing: VariantsToPed, the world's most annoying walker! And also a busted QScript to run it that I need Khalid's help debugging ( frownie face ). Note that VariantsToPed and PlinkSeq generate the same binary file (up to strand flips...thanks PlinkSeq), so I know it's working properly. Hooray!
2012-02-01 10:39:03 -05:00
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
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
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
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
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
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
2a565ebf90
embarrassing fix-up, thanks Khalid.
2012-01-26 19:58:42 -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
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
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
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
859dd882c9
Don't make it standard for now
2012-01-26 00:38:16 -05:00
c5e81be978
Adding pairwise AF table. Not polished at all, but usable none-the-less.
2012-01-26 00:37:06 -05:00
702a2d768f
Initial version of multi-allelic summary module in VariantEval
2012-01-25 19:42:55 -05:00
9a60887567
Lost an import in the merge
2012-01-25 19:41:41 -05:00
cba5f1a8b1
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2012-01-25 19:19:03 -05:00
Ryan Poplin
Mauricio Carneiro
Christopher Hartl
Eric Banks
Matt Hanna
Mark DePristo
Menachem Fromer