1896f334d9
Fixed collection of bugs in reads aligning to multiple locations.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1955 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-02 04:02:09 +00:00
af6d0003f8
-Generalized the GenotypeConcordance module to deal with any number of individuals (although it will default to its old behavior if the -samples argument is left out).
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-Make rods return the appropriate type of Genotype calls from getGenotype().
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1954 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-01 05:35:47 +00:00
b95165e39c
Make alignment (temporarily) part of main GenomeAnalysisTK.jar. Add some extra logging errors on failure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1953 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-01 00:33:18 +00:00
4b0796ba58
After fixing a few glitches and bugs, this version finally works as intended
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1952 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-31 04:59:58 +00:00
7d0ac7c6f2
Fix for long-term VariantEval bug plus new intergration test to catch it
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1951 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-31 00:00:33 +00:00
ea8d5c7077
Some internal refactoring. Now "safely" ignores duplicate records (NOT duplicate reads but rather malformed bam files!) resulting from the bug/feature in CleanedReadInjector.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1949 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 17:50:51 +00:00
a3da475c88
Documentation and cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1946 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 15:40:28 +00:00
2d15891719
Created walkers for alignment, validation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1945 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 15:04:07 +00:00
51fffc7f69
Comments for Ryan (which also apply to ReadQualityScoreWalker).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1944 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 14:44:04 +00:00
ccd7440730
We can actually make this a bit simpler (and faster)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1943 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 04:21:03 +00:00
1b6333e4ab
Enough people have asked for this that it just needed to get written.
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One can now split up any number of sets into an N-way Venn (although it doesn't check for discordance in the calls, so you'll still want to use SimpleVenn for 2-way comparisons).
Wiki docs are updated.
To do: update to use Ryan's generic hash map when it's ready for public use.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1942 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 04:08:45 +00:00
4bdb5b03bd
tell UnifiedGenotyper to return calls at all bases
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1941 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 03:10:44 +00:00
4ee1d6f733
-Have the calculation models determine whether a call passes the lod/confidence thresholds (as opposed to returning everything and letting the UG decide); this way, walkers which call map() will get only the good calls.
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-Do the right thing in all models for all-base-mode (for Kiran).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1940 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 02:35:51 +00:00
64ac956885
Okay, I caved in:
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CallsetConcordance now gets possible concordance types by looking at classes that implement ConcordanceType instead of having them hard-coded in.
Thanks to Kiran this was pretty easy...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1939 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-30 00:32:26 +00:00
1f0d852a48
Fix bug where alignments with indels would be busted because bwa reverses
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the read bases to undo a previous read base reverse that doesn't occur in the
libbwa codepath.
Also fixed some memory management issues.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1938 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 21:33:13 +00:00
e3b4d4cbed
Genotyper reimplemented. Does the same thing, at least for now, but internal data structures redesign enables collecting various statistics for indel-containing/reference-matching reads. The statistics are not yet used by the caller itself to make a better judgement w.r.t. the validity of the calls it makes, but they are now printed into the output stream (--verbose). The statistics (for both normal and tumor) include: indel observation count/total coverage, av. number of mismatches per indel-containing and per ref-matching read, av. mapping quality, av. mismatch rate and av. base quality within an NQS windoew around the indel, numbers of indel and ref observations per strand.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1936 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 19:09:16 +00:00
f04b80d7db
Fixed epic memory leak.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1934 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 16:32:43 +00:00
2b96b2e4e7
better multi-sample integration test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1933 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 13:51:51 +00:00
1c4ca9d383
-Mark just reminded me: actually force the ref/loc to be immutable
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-VCF writer should be blind to the score/confidence/lod value - just print the thing out as is
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1932 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 13:41:53 +00:00
5cdbdd9e5b
now that the design is stable, pull the setReference and setLocation methods back out of Genotype and stick them into constructors of implementing classes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1931 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 13:27:37 +00:00
3091443dc7
Sweeping changes to the genotype output system, as per several discussions with Matt & Aaron.
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Some things still need to be changed, but it will entail some more design decisions first (which means I get to bug M&A again tomorrow!).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1930 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 03:46:41 +00:00
86573177d1
Reverting rod walkers to use underlying refwalker implementation while we work on ROD2 and reenable the system. Added some serious sparse file parsing to variant eval tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1929 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 01:04:37 +00:00
c9a3707cfd
Initial version of BWA/C bindings. Still lots of squirrels roaming the code.
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- Some cigar strings aren't right.
- Memory leaks.
- BWA codebase changes aren't committed to BWA tree.
- Aligner interface butchered to support BWA/C-style alignments.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1928 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-28 21:37:49 +00:00
c4359bc340
Whoops. Forgot the implements.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1927 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-28 19:59:57 +00:00
5a3bd50537
adding error log reporting to the GATK, and a stream based output method for the argument collection
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1926 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-28 19:56:05 +00:00
863d3023d5
IndelCounterWalker -- a new little walker that counts indels over a region (want to see what kind of havoc BWA may be resulting in). Don't know when BasicPileup.indelPileup() was written, but kudos to whoever wrote it.
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BTTJ - remove 'N's from previous base analysis -- even if both read and ref are 'N' (which does happen, occasionally)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1925 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-28 19:50:50 +00:00
04e9a494e9
removed the GenotypesBacked interface, which is currently unused. Also cleaned up some documentation lines
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1924 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-28 18:08:14 +00:00
06ff81efe5
Added NeighborhoodQualityWalker.java and ReadQualityScoreWalker.java which are used to calculate a read quality score based on attributes of the read and the reads in the neighborhood.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1922 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-28 13:24:11 +00:00
68fa6da788
Initial graph-based reference implementation and alignment assessor. Not suitable for public use
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1921 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-27 21:54:47 +00:00
31d143a841
now only needs READS
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1920 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-27 21:54:14 +00:00
ef2ea79994
code cleanup and containsStartPosition function
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1919 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-27 21:53:40 +00:00
186a8dd698
Trivial protection for null value
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1918 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-27 21:52:52 +00:00
be333da9c0
charSeq2byteSeq -- convert a char[] to a byte[] for convenience
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1917 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-27 21:52:23 +00:00
4192b093b8
More robust error handling with parallelization + usePreviousBase. Added forceReadBasesToMatchRef to use in conjunction with nPreviousReadBases as a less stringent approximation of usePreviousBases (requiring previous pileups only had mismatches, and that read mapping quality be high was throwing everything away)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1916 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-27 17:20:44 +00:00
31d5df2859
Previous base now checks that the read matches the reference in the previous base window.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1915 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-27 15:58:20 +00:00
726378be8b
Almost ready to stop doing eagar decoding; waiting on Eric
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1914 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-27 15:28:05 +00:00
e96b1791ab
Need to check for biallelic snp or exception gets thrown.
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Also, update to new tracker calls.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1913 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-27 02:43:43 +00:00
3fb3773098
a fix for traverse dupplicates bug: GSA-202. Also removed some debugging output from FastaAltRef walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1912 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-26 20:18:55 +00:00
a1e8a532ad
Support for initialize() and onTraversalDone() output from parallelized walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1911 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-26 20:18:31 +00:00
62c1001790
BTTJ is now correct. What a terrible waste of time, turns out I'd just reversed the header. Because of this the MD5 had to be updated in the tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1910 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-26 19:24:18 +00:00
24c7f694e6
Handles allele frequencies for any specified population, changed user input for mismatch filter options
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1909 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-25 22:51:56 +00:00
db9419df49
@ Hack to allow output from onTraversalDone()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1908 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-25 15:19:04 +00:00
75ad6bbef7
Check that map isn't being called passing in null arguments.
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(This seems wrong; see JIRA entry GSA-211)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1907 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-25 02:30:36 +00:00
b4f55df600
Bugfix for Jason F
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1906 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-24 22:09:27 +00:00
65b98470f3
Temporary fix: have RodLocusView manage and close its RODs. Really the
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relationship between these two classes needs to be rethought; see JIRA
GSA-207.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1904 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-23 16:00:12 +00:00
ad1fc511b1
intermediate commit for some changes in the Variation system, so Eric can go ahead with his changes. Everything is pretty set, but the Variation interface could use a convenience method that joins all the alternate alleles.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1903 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-23 06:31:15 +00:00
6c338eccb8
Joint Estimation model now emits calls in all formats.
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The whole GenotypeCall framework needs to be changed, but this will work for the time being.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1902 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-23 03:07:28 +00:00
a6dc8cd44e
BTTC is now Tree Reducible allowing for parallelization.
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Integration test comment changed to reflect actual date of last md5 update.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1901 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-22 23:19:29 +00:00
2e552eb5a1
Validates intervals against sequence dictionary header bounds.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1900 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-22 19:31:15 +00:00
54c61c663c
-Cleanup of the Joint Estimation code
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-Don't print verbose/debugging output to logger, but instead specify a file in the argument collection (and then we only need to print conditionally)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1899 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-22 15:25:29 +00:00
hanna
ebanks
asivache
depristo
chartl
aaron
rpoplin
sjia