1b722c21cf
merge master
2011-10-25 16:08:39 -04:00
9eaa62f3f3
Tmp. SAM-JDK rev. Better google caliper example
2011-10-25 15:15:52 -04:00
2794e5c1d4
Modified the VCFJarClassLoadingUnitTest to play nice with the packaged-jar test targets.
2011-10-25 14:47:15 -04:00
b559936b7a
a)New variant eval stratification module for indel size. b) Next iteration on indel caller runtime optimization: when computing likelihood of each haplotype for a given read, many computations will be redundant since pieces of haplotypes will be common to both REF and ALT haplotypes. So, we keep HMM matrices from one haplotype to the next one and recompute starting at the part where either haplotype is different or GOP/GCP are different.
2011-10-25 09:56:43 -04:00
bf61393a7d
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-25 07:47:22 -04:00
9afe6fc7ac
Picard upgrade to 1.55.
2011-10-24 17:02:27 -04:00
fac9932938
Embedding gsalib source and queueJobReport R scripts in the dist and package jars.
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Moved gsalib and queueJobReport.R to embeddable namespaced locations.
Updated packager dependencies/dir to add an @includes which filters the embedded fileset.
RScriptExecutor can now JIT compiles the gsalib.
RScriptExecutor uses ProcessController and sends the Rscript output to java's stdout when run under -l DEBUG.
Refactored ProcessController and IOUtils from Queue to Sting Utils.
Added more unit tests to ProcessController along with a utility class to hard stop OutputStreams at a specified byte count.
Replaced uses of some IOUtils with Apache Commons IO.
ShellJobRunner refactored to use direct ProcessController and now kills jobs on shutdown.
Better QGraph responsiveness on shutdown by using Object.wait() instead of Thread.sleep().
2011-10-24 15:58:34 -04:00
89a581a66f
Added ability to specify arguments in files via -args/--arg_file
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Pushing back downsample and read filter args so they show up in getApproximateCommandLineArgs()
2011-10-24 15:58:34 -04:00
502592671d
Cleanup FragmentPileup before main repo commit
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-- removed intermiate functions. Now only original version and best optimized new version remain
-- Moved general artificial read backed pileup creation code into ArtificialSamUtils
2011-10-24 14:40:05 -04:00
166174a551
Google caliper example execution script
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-- FragmentPileup with final performance testing
2011-10-24 14:04:53 -04:00
f6ccac889b
Merged bug fix from Stable into Unstable
2011-10-23 16:37:12 -04:00
585a45b7a3
Bug fix for ClipReadsWalker when stats output isn't provided
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-- See http://getsatisfaction.com/gsa/topics/clipreadswalker?utm_content=topic_link&utm_medium=email&utm_source=reply_notification
2011-10-23 16:36:48 -04:00
42bf9adede
Initial version of "fast" FragmentPileup code
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-- Uses mayOverlapRoutine in ReadUtils
-- Attempts to be smart when doing overlap calculation, to avoid unnecessary allocations
-- PileupElement now comparable (sorts on offset than on start)
-- Caliper microbenchmark to assess performance
2011-10-22 21:36:37 -04:00
c3cb07fc1d
Relocating the ReduceBAM script.
2011-10-22 13:35:52 -04:00
4913f8a60f
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-21 17:45:07 -04:00
86305a5dcf
Adjusting the memory limits of the MDCP
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Indel caller needs more than 3G for large datasets.
2011-10-21 17:41:52 -04:00
102dafdcbc
Validation of GATKSamRecord in read filters
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Moved the validation of the GATKSamRecord to the MalformedReadFilter with the intent to make the read filter the ultimate validation location for sam records. This way we can opt to filter out malformed reads if we know what we are doing or blow up otherwise.
2011-10-21 17:40:43 -04:00
f4b409fa0d
CombineVariants bug fix: when merging records with disparate alleles we were leaving AC,AF fields intact. This had as a consequence that we could end up with a record with 3 alt alleles but only 2 values in AC,AF fields. Now, if alleles in combined vc are different from original, and if AC,AF fields can't be recomputed from genotypes, we remove attributes from vc map since they'll be invalid anyway. Integration test md5 changed since there were several badly merged records in result
2011-10-21 14:07:20 -04:00
b863390cb1
Moving reduced read functionality into GATKSAMRecord
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-- More functions take / produce GATKSAMRecords instead of SAMRecord
2011-10-21 13:28:05 -04:00
1b01e24e23
Moving around comments
2011-10-21 13:26:30 -04:00
2403e96062
Renamed GATKSamRecord -> GATKSAMRecord for consistency. Better docs.
2011-10-21 09:59:24 -04:00
110e13bc1e
Merge branch 'master' into SamRecordFactory
2011-10-21 09:43:52 -04:00
be797a8a1f
Recalibrator now uses the much more efficient NGSPlatform in the cycle covariates system
2011-10-21 09:39:21 -04:00
ed74ebcfa1
GATKSamRecords with efficiency NGSPlatform method
2011-10-21 09:38:41 -04:00
94e1898d8f
A canonical set of NGS platforms as enums with convenient manipulation methods
2011-10-21 09:37:45 -04:00
9f867d77ca
no sort order
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subtle bug fixed.
2011-10-20 18:44:09 -04:00
c9d8b22092
Added BWASW support to the pipeline
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Data Processing Pipeline can now use BWASW for realigning the reads. Useful for Ion Torrent data.
2011-10-20 18:36:28 -04:00
093cd95c5d
Merged bug fix from Stable into Unstable
2011-10-20 17:03:22 -04:00
d7367c152a
Fixing 'revert' when not realigning
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RevertSam was reverting the alignment information and that was screwing up the pipeline if you didn't want to run it with BWA. Fixed.
2011-10-20 17:01:54 -04:00
558a7a81f0
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-20 16:23:32 -04:00
ed402588cc
Adding the "gold standard NA12878" target
2011-10-20 16:19:13 -04:00
6f72b3de6a
Forgot to add this in too (oops)
2011-10-19 18:46:31 -04:00
999a8998ae
Constructor for GATKSamRecord with header only, for unit testing
2011-10-19 17:51:48 -04:00
3227143a1c
Systematic test code for FragmentPileup
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-- Creates all combinatinos of overlapping and non-overlapping read pair pileups in all orientations and first/second pairings to validate fragment detection.
2011-10-19 17:50:27 -04:00
bba69701b5
Now creates GATKSamRecords now SamRecords
2011-10-19 17:49:17 -04:00
cd8a6d62bb
You know how the wiki has a big section on commiting local changes to BRANCHES of the repository you clone it from? Yeah. It sucks if you don't do that.
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This commit contains:
- IntronLossGenotyper is brought into its current incarnation
- A couple of simple new filters (ReadName is super useful for debugging, MateUnmapped is useful for selecting out reads that may have a relevant unaligned mate)
- RFA now matches my current local repository. It's in flux since I'm transitioning to the new traversal type.
+ the triggering read stash pilot required me to change the scope of some of the variables in the ReadClipping code, private -> protected. Those are all the changes there.
- MendelianViolation restored to its former glory (and an annotator module that uses the likelihood calculation has been added)
+ use this rather than a hard GQ threshold if you're doing MV analyses.
- Some miscellaneous QScripts
2011-10-19 17:42:37 -04:00
52345f0aec
Meaningful documentation string
2011-10-19 15:47:36 -04:00
1b38aa1a7e
Cleaning up reduced read code accessors
2011-10-19 15:46:44 -04:00
d8d73fe4f2
Treat ./X genotypes as MIXED so that isHet, isHom, etc. still return the expected and correct values. Added docs to these accessors with contracts explicitly mentioned. Fixed case where NPE could be thrown.
2011-10-19 15:11:13 -04:00
7928b287fc
GATKSamRecord now produced by SAMFileReaders by default
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-- Removed all of the unnecessary caching operations in GATKSAMRecord
-- GATKSAMRecord renamed to GATKSamRecord for consistency
2011-10-19 13:15:27 -04:00
5a6468c11e
Allowing ./X genotypes and adding a unit test to ensure that this case is covered from now on (especially given that we may want to revert in the future). Reverting this change is really easy and entails uncommenting a few lines of code. But for now, despite Mark's objections, this case is allowed in the VCF spec and we are wrong not to allow it.
2011-10-19 11:52:05 -04:00
48c4a8cb33
Make error messages clearer (even I was confused)
2011-10-19 11:49:16 -04:00
6cadaa84c9
Just use validate() from super class since it does the same thing
2011-10-19 11:48:23 -04:00
df3e4e1abd
First working code to use SamRecordFactory to produce objects of our own design in SAMFileReader
2011-10-19 11:22:35 -04:00
d79b57d6f4
Fixing cases where the Object equals function wasn't being properly overridden in the haplotype caller classes.
2011-10-19 08:57:38 -04:00
c27e2fb676
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-18 15:23:05 -04:00
2125c4f38f
Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-18 14:49:00 -04:00
e5fc828546
With Khalid's implicit approval, I have removed this line that overrides the memory limit of the VCF-gathering function, so that the inherited limit remains
2011-10-18 14:47:39 -04:00
f77f2eeb7d
Fix for new ID structure
2011-10-18 13:04:43 -04:00
1a92ee3593
No longer adds a binding of ID -> . when the ID field is dot in the VCF
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-- Really we should make ID a primary key in VariantContext. Putting it into the attributes is just annoying now
2011-10-18 10:57:02 -04:00
Mark DePristo
David Roazen
Guillermo del Angel
Matt Hanna
Khalid Shakir
Mauricio Carneiro
Christopher Hartl
Eric Banks
Ryan Poplin
Menachem Fromer