660998065b
'Okay, now I'm absolutely certain that there are no more bugs in the constrained writer.'
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5353 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-02 03:48:40 +00:00
05fac8583d
Following up Mark's recent commit: hooking up the --maxPositionalMoveAllowed argument into the indel realigner and through to the SAM writer. We now ensure that no read is realigned more than N bases (200 by default, which is nowhere close to realistically possible). If anyone ever sees a warning message about this with the default value then please let me know because I need to see it for myself.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5331 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-28 04:40:54 +00:00
1dedfdb11b
Fixes for constrained movement Indel Realigner. Now sorts all of the reads in the interval before handing them to ConstrainedMateFixingSAMFileWriter to maintain correct contract between the two pieces of software
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5329 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-28 03:52:18 +00:00
5d28cbda27
When crossing contigs it's crucial that the queue get flushed or else it will continue to accumulate reads without emitting. This is the last time I trust someone when they tell me that they are 'confident there are no bugs' in a tool.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5315 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-25 05:18:30 +00:00
1129f1535d
Fix for the HaplotypeScore optimization in AlignmentUtils
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5310 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-24 20:40:18 +00:00
255cc246a2
Change in Methods development pipeline: dbsnp130 can't be used for anything, changed it to dbsnp129. Optimization for HaplotypeScore and the to-be-committed ReadRosRankSumTest in AlignmentUtils
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5301 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-24 16:09:03 +00:00
93888e570b
Phase 2: after hours of testing, confirming that constrained mode looks good so moving the integration tests over to use it. Some cleanup. More cleanup coming in Phase 3.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5298 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-24 06:23:41 +00:00
29f3ad72f3
SAMFileWriter that allows the user to move reads, but only a bit, in an incoming coordinated sorted BAM files. Does some local reordering and local mate fixing, under specified constrained. These constrains allow us to make a special -- under testing for Eric, who promised to try this out a bit, expand test cases and integration tests -- but soon to be the default and only model of the realigner that only moves reads with ISIZE < 3000 that directly emits a coordinate sorted, mate fixed validating BAM file without needing FixMates externally. Preliminary testing shows this runs in a totally fine amount of memory and produces equivalent results to the previous version.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5199 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 22:27:05 +00:00
0ad1ea4aa1
Fixed Umapped misspelling
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5196 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-04 22:21:41 +00:00
862b299b47
Fix Picard OTF index generation issue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5077 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-26 03:42:46 +00:00
ce3d226183
Reverting back to the old definition of QD because it works better with large numbers of samples. The new QD is relegated to a new annotation: sumGLbyD. Tweaks to the new HaplotypeScore based on evaluation with better QD calculation. The default qual threshold in GenerateVariantClusters is updated to be in line with the variant quality scores coming from the exact model.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4984 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-13 14:12:30 +00:00
5e9a8f9cb3
Implemented a new argument (-DQS --defaultQualityScore) that allows GATK to deal with BAM files missing quality scores. If a value is specified, all reads are filled with the default quality score. Appropriate exception is thrown if -DQS is not provided and BAM file doesn't have quality scores for every base.
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Adding the first version of the techdev pipeline (tdPipeline)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4943 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-05 22:25:08 +00:00
23dbc5ccf3
HaplotypeScore is revamped. It now uses reads' Cigar strings when building the haplotype blocks to skip over soft-clipped bases and factor in insertions and deletions. The statistic now uses only the reads from the filtered context to build the haplotypes but it scores all reads against the two best haplotypes. The score is now computed individually for each sample's reads and then averaged together. Bug fixes throughout. The math for the base quality and mapping quality rank sum tests is fixed. The annotations remain as ExperimentalAnnotations pending more investigation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4934 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-05 00:28:05 +00:00
8d2c14b29c
Update Picard / sam-jdk at Tim's request.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4925 348d0f76-0448-11de-a6fe-93d51630548a
2011-01-03 02:17:25 +00:00
cf7d932a17
Fix for f***ed up BWA alignments that adhere to SAM specs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4834 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-14 17:12:25 +00:00
8e36a07bea
Convert GenomeLocParser into an instance variable. This change is required
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for anything that needs to be simultaneously aware of multiple references, eg
Queue's interval sharding code, liftover support, distributed GATK etc.
GenomeLocParser instances must now be used to create/parse GenomeLocs.
GenomeLocParser instances are available in walkers by calling either
-getToolkit().getGenomeLocParser()
or
-refContext.getGenomeLocParser()
This is an intermediate change; GenomeLocParser will eventually be merged
with the reference, but we're not clear exactly how to do that yet. This
will become clearer when contig aliasing is implemented.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4642 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-10 17:59:50 +00:00
181f901126
Fix for Ryan: don't pull reference sequence for the portions of reads that extend beyond the contig boundaries
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4551 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-22 14:38:26 +00:00
2606e67cf1
Reverting Matt's change from yesterday which I accidentally blew away when trying to cope with the stupid svn update issues we've been plagued with recently.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4495 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-14 14:40:42 +00:00
cfb33d8e12
Filtering optimizations are now live for UGv2. Instead of re-computing filtered bases at every locus, they are computed just once per read and stored in the read itself. Eyeballing the results on the ~600 sample set from 1kg, we cut out ~40% of the runtime! QUALs are now sometimes different from UGv1 because I noticed a bug in v1 where samples with spanning deletions only were assigned ref calls instead of no-calls which ever so slightly affects the QUAL. Not a big deal though.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4494 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-14 05:04:28 +00:00
83b8676b69
Hack to fix mysterious disappearing read attributes. Ultimately caused
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by the fact that the GATKSAMRecord, by design, needs to both inherit from
SAMRecord and wrap a 'member' SAMRecord, and method calls that aren't
implemented as explicit passthroughs can compromise the content of the
SAMRecord in subtle ways.
Will be automatically fixed when Picard moves to a lightweight SAMRecord
interface rather than the current heavyweight implementation. But in
the short-term, there's no obvious fix.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4489 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-13 19:06:54 +00:00
530875817f
Experimental code for better filtering of bases in sam records. Not hooked up yet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4475 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-11 02:19:51 +00:00
39e373af6e
deleting accidentally committed junk
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4464 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-08 15:13:01 +00:00
edaa278edd
Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance.
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This will allow other programs like Queue to reuse the functionality.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4351 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-25 02:49:30 +00:00
7880863eb7
Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4267 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 15:07:38 +00:00
7ad8fbdd5a
Moved GATKException to exceptions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4266 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 14:47:19 +00:00
595907e98e
Moving StingException
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4262 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 14:34:15 +00:00
40e6179911
Penultimate step in exception system overhaul. UserError is now UserException. This class should be used for all communication with the USER for problems with their inputs. Engine now validates sequence dictionaries for compatibility, detecting not only lack of overlap but now inconsistent headers (b36 ref with v37 BAM, for example) as well as ref / bam order inconsistency. New -U option to allow users to tolerate dangerous seq dict issues. WalkerTest system now supports testing for exceptions (see email and wiki for docs). Tests for vcf and bam vs. ref incompatibility. Waiting on Tribble seq dict improvements to detect b36 VCF with b37 ref (currently cannot tell this is wrong.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4258 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 14:02:43 +00:00
8f1a32acae
All exceptions thrown by the GATK have been reviewed and UserErrors replaced where appropriate. Shazam. Another check-in will remove the GATKException and restore the StingException.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4252 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-10 15:25:30 +00:00
41d57b7139
Massive cleanup of read filtering.
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- Eliminate reduncancy of filter application.
- Track filter metrics per-shard to facitate per merging.
- Flatten counting iterator hierarchy for easier debugging.
- Rename Reads class to ReadProperties and track it outside of the Sting iterators.
Note: because shards are currently tied so closely to reads and not the merged triplet of <reads,ref,RODs>, the metrics
classes are managed by the SAMDataSource when they should be managed by something more general. For now, we're hacking
the reads data source to manage the metrics; in the future, something more general should manage the metrics classes.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4015 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-11 20:17:11 +00:00
012a7cf0a5
mismatchCount now has a version that counts mismatches only along a part of the read (takes additional args start_on_read and length_on_read to specify the read's subsequence to be interrogated);
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isMateUnmapped() convenience shortcut method added.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3931 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-04 15:27:35 +00:00
3308d956f4
Added utility shortcut method: getOriginalQualsInCycleOrder(read)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3851 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-22 15:44:25 +00:00
8e31c01680
Solid processing in base quality recalibrator now has several options for how to handle no calls in the color space. --ignore_nocall_colorspace is removed and replace by --solid_nocall_strategy. Fixed some of the @Deprecated tags in BaseUtils. LocusWalkers now filter out FailsVendorQualityCheck reads. HLA caller integration test bam file had bad vendor reads so its integration test changed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3831 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-19 19:10:29 +00:00
bd2ba3eb37
deal with very large known indels that fall off our ref context
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3745 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 20:05:16 +00:00
47a42b1507
trivial cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3736 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-08 04:42:32 +00:00
be8740b00d
Another edge case in left alignment for indels: deal with cases when insertions are ambiguously placed at ends of reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3715 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-04 17:26:38 +00:00
003dd4de3e
Rev Picard with performance enhancements.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3615 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 22:54:23 +00:00
612c3fdd9d
First pass at eliminating the old sharding system. Classes required for the original sharding system
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are gone where I could identify them, but hierarchies that split to support two sharding systems have
not yet been taken apart.
@Eric: ~4k lines.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3580 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-17 20:17:31 +00:00
e2b41082af
GATK now does automatic adaptor filtering in locus iterators (but not expt. downsampling iterator). General support for LocusIteratorFilters just like read filters but only applying at particular bases. Updated tools with new MD5 sums due to adaptor bases in their integrationtest data. Not that as a side effect here reads close to each other with odd orientations are also filtered out. Updated minor argument to VariantRecalibrator to change the qStep value on the command line
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3481 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 22:26:32 +00:00
4a555827aa
Removing more toUpperCase sanity checks
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3471 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-02 14:38:39 +00:00
2b02324587
Support for detecting and automatically excluding reads reading into the adaptor sequence and, if desired, also only showing the first pair when two reads overlap in the fragment. Not enabled, an intermediate check in before updating and verifying the impact on locus walkers everywhere.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3465 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-30 18:00:12 +00:00
5928047d8b
Optimization of reference window calculation to us bytes not char and no uppercasing since reference and read bases are always uppercase now. Should remove some ~5% of runtime of UG.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3438 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-26 14:10:26 +00:00
772f558ae0
Massive change to the indel realigner code. We now properly deal with soft-clipped reads. Also, improved left-alignment code.
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Small change for Ryan to get hard-clipped reads working for the recalibrator.
PLEASE DO NOT RELEASE THIS WEEK. I still have some more testing to do and need Mark to run WG jobs.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3430 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-25 20:04:33 +00:00
727822adb4
BaseUtils has more clear distinction between byte and char routines. All char routines are @Depreciated now. Please use bytes. Better organization of reverse(), now in Utils not BaseUtils.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3400 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-20 14:05:13 +00:00
8a725b6c93
Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3397 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-19 23:27:55 +00:00
76efa757f0
Switched over to reviewed version of Picard patch. In process, did some optimization to the IntervalSharder
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which improved startup time 5-10x when dynamically merging many BAMs.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3331 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-08 14:12:22 +00:00
64640d6b17
Complete the switch statement to deal with all possible cigar operators for Kris.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3299 348d0f76-0448-11de-a6fe-93d51630548a
2010-05-05 13:41:05 +00:00
42bcca1010
Pulling out the left-alignment code for indels so that other walkers can use it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3251 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 16:12:34 +00:00
32d86cf457
Rev the reservoir downsampler to support partitioning through a functor.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3232 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-21 19:50:26 +00:00
c1e53d407d
The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
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unicode quote characters embedded in it. These characters were invisible inside
IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason
have a different default charset. Fixed.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3203 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-20 15:26:32 +00:00
1bc26f69e9
An attempt to cleanup the Utils directory. Email to follow.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3198 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-19 23:00:08 +00:00
ebanks
depristo
rpoplin
hanna
carneiro
asivache
kshakir