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1734 Commits (6fe1c337ff9d05bf796abb8924fa2dbb50e4f93d)

Author SHA1 Message Date
depristo 7d0ac7c6f2 Fix for long-term VariantEval bug plus new intergration test to catch it 
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
asivache ea8d5c7077 Some internal refactoring. Now "safely" ignores duplicate records (NOT duplicate reads but rather malformed bam files!) resulting from the bug/feature in CleanedReadInjector. 
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
hanna a3da475c88 Documentation and cleanup. 
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
hanna 2d15891719 Created walkers for alignment, validation. 
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
ebanks 51fffc7f69 Comments for Ryan (which also apply to ReadQualityScoreWalker). 
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
ebanks ccd7440730 We can actually make this a bit simpler (and faster) 
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
ebanks 1b6333e4ab Enough people have asked for this that it just needed to get written. 
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
ebanks 4bdb5b03bd tell UnifiedGenotyper to return calls at all bases 
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
ebanks 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. 
-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
ebanks 64ac956885 Okay, I caved in: 
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
hanna 1f0d852a48 Fix bug where alignments with indels would be busted because bwa reverses 
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
asivache 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. 
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
hanna f04b80d7db Fixed epic memory leak. 
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
ebanks 2b96b2e4e7 better multi-sample integration test 
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
ebanks 1c4ca9d383 -Mark just reminded me: actually force the ref/loc to be immutable 
-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
ebanks 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 
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
ebanks 3091443dc7 Sweeping changes to the genotype output system, as per several discussions with Matt & Aaron. 
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
depristo 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 
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
hanna c9a3707cfd Initial version of BWA/C bindings. Still lots of squirrels roaming the code. 
- 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
chartl c4359bc340 Whoops. Forgot the implements. 
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
aaron 5a3bd50537 adding error log reporting to the GATK, and a stream based output method for the argument collection 
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
chartl 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. 
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
aaron 04e9a494e9 removed the GenotypesBacked interface, which is currently unused. Also cleaned up some documentation lines 
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
rpoplin 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. 
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
depristo 68fa6da788 Initial graph-based reference implementation and alignment assessor. Not suitable for public use 
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
depristo 31d143a841 now only needs READS 
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
depristo ef2ea79994 code cleanup and containsStartPosition function 
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
depristo 186a8dd698 Trivial protection for null value 
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
depristo be333da9c0 charSeq2byteSeq -- convert a char[] to a byte[] for convenience 
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
chartl 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) 
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
chartl 31d5df2859 Previous base now checks that the read matches the reference in the previous base window. 
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
depristo 726378be8b Almost ready to stop doing eagar decoding; waiting on Eric 
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
ebanks e96b1791ab Need to check for biallelic snp or exception gets thrown. 
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
aaron 3fb3773098 a fix for traverse dupplicates bug: GSA-202. Also removed some debugging output from FastaAltRef walker 
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
hanna a1e8a532ad Support for initialize() and onTraversalDone() output from parallelized walkers. 
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
chartl 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. 
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
sjia 24c7f694e6 Handles allele frequencies for any specified population, changed user input for mismatch filter options 
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
chartl db9419df49 @ Hack to allow output from onTraversalDone() 
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
ebanks 75ad6bbef7 Check that map isn't being called passing in null arguments. 
(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
depristo b4f55df600 Bugfix for Jason F 
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
hanna 65b98470f3 Temporary fix: have RodLocusView manage and close its RODs. Really the 
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
aaron 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. 
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
ebanks 6c338eccb8 Joint Estimation model now emits calls in all formats. 
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
chartl a6dc8cd44e BTTC is now Tree Reducible allowing for parallelization. 
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
hanna 2e552eb5a1 Validates intervals against sequence dictionary header bounds. 
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
ebanks 54c61c663c -Cleanup of the Joint Estimation code 
-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
asivache 2cab4c68d4 Added method: isCodingExon(). Returns true if position is simultaneously within an exon AND within coding interval of any single transcript from the list. The old method of detecting coding positions as isExon() && isCoding() is buggy, as the position could be in the UTR part of one transcript (isExon() is true), and within coding region bounds (but not in the exon) of another transcript (isCoding() is true). As a result UTR positions would be erroneously annotated as coding. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1898 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-22 14:55:07 +00:00
chartl af761fb9bd Base transition table now forces epsilon/3 (three-state) model for the unified genotyper. Verified to be identical with changing the default model to being epsilon/3. This of course changes the observed counts, so the integration test has been updated. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1897 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-21 21:18:26 +00:00
ebanks 55fa1cfa06 -Renamed new calculation model and worked out some significant xhanges with Mark 
-Allow walkers calling the UG to pass in their own argument collections


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1896 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-21 20:49:36 +00:00
chartl 8e3f72ced9 BTTJ - Code refactoring (major) - passes integration test 
VariantEvalWalker - whoops, wrote PooledGenotypeAnalysis rather than PooledAnalysis, now passes tests again

- PooledFrequencyAnalysis - don't bother initializing matrices if this isn't a pool




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1895 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-21 19:04:51 +00:00
depristo 15a1849758 notes for chartl 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1894 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-21 18:31:31 +00:00
chartl 77863d4940 @PowerBelowFrequency 
+ Changes to doc

@ BasicPoolVariantAnalysis
    + use char rather than ReferenceContext
    + calculate # alleles

@ PooledFrequencyAnalysis
    + breakdown of call metrics by estimated number of alleles in pool

@ VariantEvalWalker
    + add PooledFrequencyAnalysis to analysis set

@ PooledGenotypeConcordance
    + correctly calculate maximal allele frequency for output




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1893 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-21 15:17:11 +00:00
chartl 967128035e Make command like args default to false. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1892 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-21 13:59:35 +00:00
ebanks 9b9744109c Mark's new unified calculation model is now officially implemented. 
Because it doesn't actually use EM, it's no longer a subclass of the EM model.

Note that you can't use it just yet because it doesn't actually emit calls (just prints to logger).  I need to deal with general UG output tomorrow.  Hold off until then, Mark, and then you can go wild.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1891 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-21 02:39:23 +00:00
depristo caa3187af8 Enabling correct high-performance ROD walker and moved VariantEval over to it. Performance improvements in variantEval in general. See wiki for full description 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1890 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 23:31:13 +00:00
chartl 4a8a6468be Use read group as a condition for confusion tables. With an integration test. 
Changed BaseTransitionTable to comparable objects for consistent ordering of output
( e.g. so the integration test doesn't yell so much )




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1889 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 19:39:32 +00:00
chartl b83df5616a Change for lower-case references (always compare upper case bases) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1888 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 17:36:31 +00:00
chartl 3b1fabeff0 Major code refactoring: 
@ Pooled utils & power
   - Removed two of the power walkers leaving only PowerBelowFrequency, added some additional
     flags on PowerBelowFrequency to give it some of the behavior that PowerAndCoverage had
   - Removed a number of PoolUtils variables and methods that were used in those walkers or simply
     not used
   - Removed AnalyzePowerWalker (un-necessary)
   - Changed the location of Quad/Squad/ReadOffsetQuad into poolseq

@NQS
   - Deleted all walkers but the minimum NQS walker, refactored not to use LocalMapType

@ BaseTransitionTable
   - Added a slew of new integration tests for different flaggable and integral parameters
   - (Scala) just a System.out that was added and commented out (no actual code change)
   - (Java) changed a < to <= and a boolean formula


Chris



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1887 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 14:58:04 +00:00
aaron 4be6bb8e92 added a check to ensure the eval track variation is bi-allelic. Also changed some string constants over to enums. For some reason my check-ins from home wouldn't work last night, so this is the actual changes for 1884. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1886 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 14:15:33 +00:00
depristo 449a6ba75a Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1885 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 12:23:36 +00:00
aaron d749a5eb5f added a check to ensure the eval track variation is bi-allelic. Also changed some string constants over to enums 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1884 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 04:56:51 +00:00
ebanks b8ab77c91c Don't filter out reads without proper read groups. Instead, allow the user (or another walker calling UG) to specify an assumed sample to use (but then we assume single-sample mode). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1883 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 01:30:53 +00:00
depristo a8a2c1a2a1 Replaced SSG with UG in packaging utils. Minor performance and formatting improvements for ClipReads 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1882 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 01:19:58 +00:00
ebanks c29924e7cf Reverting previous change. 
Aaron, it's all yours...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1881 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 00:55:24 +00:00
aaron d21b582b18 memory leak, where the Resource Pool was releasing based on the value and not the key, resulting in the resourceAssignments map growing with each additional shard 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1880 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 00:39:42 +00:00
ebanks 761a730758 assertBiAllelic -> assertMultiAllelic. 
Chris, if this breaks an integration test, you get it.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1879 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-20 00:09:46 +00:00
depristo 2a26bb42dd Softclipping support in clip reads walker. Minor improvement to WalkerTest -- now can specify file extensions for tmp files. Matt -- I couldn't easily create non-presorted SAM file. The softclipper has an impact on this. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1878 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-19 21:54:53 +00:00
chartl 055a99fb05 Change in ordering for a disjunctions. Walker will no longer try to calculate number of simple mismatches in the pileup if the pileup includes 'N's. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1877 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-19 18:24:14 +00:00
chartl 10bde9e77b Integration test for BTT calculator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1876 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-19 18:21:55 +00:00
aaron cfa86d52c2 ensure that in the indel case we don't allow identification as both an insertion and deletion at the same location in the VCF ROD 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1875 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-19 18:21:00 +00:00
chartl 3d50c72d74 Forgot a dumb little System.out.println. You will be flooded with "This read will not be used." statements until, overwhelmed, you give in to my demands. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1874 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-19 16:13:48 +00:00
chartl 225ef52973 Now produces same output as the Scala walker for unconditioned tables (no 2bb, no previous base, etc.) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1873 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-19 16:10:44 +00:00
ebanks bb180a23ef Updated MD5 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1871 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-18 05:30:38 +00:00
ebanks 51f9ec0a5c subtract largest posterior value from all values; this hopefully solves any precision issues 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1870 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-18 05:20:15 +00:00
ebanks b9e8867287 -push allele frequency and genotype likelihood variable definitions down into the subclasses so that they can use different data structures 
-use slightly more stringent stability metric
-better integration test



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1869 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-18 04:22:17 +00:00
depristo d6385e0d88 simpleComplement function() in BaseUtils. Generic framework for clipping reads along with tests. Support for Q score based clipping, sequence-specific clipping (not1), and clipping of ranges of bases (cycles 1-5, 10-15 for example). Can write out clipped bases as Ns, quality scores as 0s, or in the future will support softclipping the bases themselves. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1868 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 22:29:35 +00:00
chartl ad777a9c14 @BasicPileup - made the counts public so they can be used 
@PoolUtils - split reads by indel/simple base

@BaseTransitionTable - complete refactoring, nicer now

@UnifiedArgumentCollection - added PoolSize as an argument

@UnifiedGenotyper - checks to ensure pooled sequencing uses the appropriate model

@GenotypeCalculationModel - instantiates with the new PoolSize argument




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1867 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 21:56:56 +00:00
andrewk bdb34fcf38 Updated integration tests for VariantEval. Hooray for IT! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1866 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 20:00:29 +00:00
aaron 41a95cb3f0 fixing unified genotyper test for change: VCF output now emits no calls as ./. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1865 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 19:38:58 +00:00
hanna 85a4fbc256 Bumping version of Picard for firehose compatibility. 
Integration tests were validated against svn rev 1861, before the wonder
twins committed their changes.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1864 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 19:38:56 +00:00
aaron 8aacc43203 VCF output now emits no calls as ./. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1863 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 18:51:31 +00:00
andrewk d1a4cd2f73 Added ValidationData analysis type to VariantEvalWalker; this eval takes a GFF file with validated truth data positions (bound to "validation")and calculates the accuracy of the genotype calls bound to "eval". 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1862 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 15:39:08 +00:00
ebanks 07b134a124 Added some integration tests for multiple samples 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1861 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 15:22:10 +00:00
ebanks 418e007ca6 A cleaner interface: now everyone can use UG's initialize method 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1860 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 14:09:16 +00:00
aaron 96972c3a5c a fix for a bug Eric found: if your first call contains fewer samples than calls at other loci, your VCFHeader got setup incorrectly. 
Also moved a buch of Lists over to Sets for consistancy.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1859 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 04:57:50 +00:00
aaron a69ea9b57c Cleaning up the VCF code, adding lots of tests for a variety of edge cases. Two issues are still outstanding: updating the no call string with the standard 1000g decided on today, and fixing Eric's issue where not all the VCF sample names are present initially. 
also: their, I hope your happy Eric, from now on I'll try not to flout my awesomest grammer in the future accept when I need to illicit a strong response :-)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1858 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 04:11:34 +00:00
ebanks b82c3b6040 Better error output (and fixed spelling mistakes) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1857 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 01:01:45 +00:00
ebanks 993c567bd8 I had to remove some of my more agressive optimizations, as they were causing us to get slightly different results as MSG. Results in only small cost to running time. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1856 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-16 00:59:32 +00:00
asivache 7d7ff09f54 throw an exception if read has no associated read group 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1855 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-15 18:11:32 +00:00
chartl b9544d3f89 Output formatting change (very slight) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1854 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-15 16:47:29 +00:00
hanna 839c5d66bc Read uints directly into longs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1853 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-15 16:15:11 +00:00
hanna ce38fa7c81 Breaking the signed int glass ceiling; stage 1: convert critical ints to longs. Code cleanup and documentation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1852 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-15 15:28:56 +00:00
kcibul 79993be46c changed blank gene name to UNKNOWN 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1851 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-15 13:47:00 +00:00
depristo 0c2016c19a Improved error messages -- now easier to read, points to the GATK Error Messages wiki, and avoids double printing of stack traces 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1850 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-15 12:07:44 +00:00
aaron a9094c835c clean-up and fixes to the VCF input 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1849 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-15 04:53:59 +00:00
ebanks a32470cea1 Deal with the fact that walkers can call UG's init/map functions directly. 
We need to filter contexts in that case since the calling walkers don't get UG's traversal-level filters.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1848 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-15 02:31:45 +00:00
hanna 8dca236958 Base-packed reader cleanup. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1847 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-15 01:26:23 +00:00
hanna 316b30ee56 On the road to human: make sure the suffix array will fit in a Java array. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1846 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 21:45:35 +00:00
ebanks e740e7a7ce Because walkers call UG's map function, we need to move the actual writing out 
to UG's reduce function.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1845 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 20:49:26 +00:00
kcibul 825e6c7a4d added calculation for bases over 2x,10x,20x,30x plus gene name 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1844 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 20:32:26 +00:00
aaron 727b69fce0 catch null output destinations earlier 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1843 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 20:07:15 +00:00
chartl 1f66738c8e Fix a hashing function bug. Ignore reads with non-reference bases in the pileup. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1842 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 19:41:26 +00:00
hanna 72c34f11dd Bug fixing for BWA output formats. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1841 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 19:32:22 +00:00
aaron 60183229ab the oldest java mistake in the book... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1840 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 19:32:13 +00:00
ebanks 52d2e0ca07 All walkers now use read.getReadGroup() 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1839 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 19:27:40 +00:00
chartl 0a09fa4d5c Rename to distinguish this transition table calculator from the scala version. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1838 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 18:52:21 +00:00
chartl 1d055011bd Getting rid of this so I can rename it without the world blowing up. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1837 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 18:45:11 +00:00
aaron eb90e5c4d7 changes to VCF output, and updated MD5's in the integration tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1836 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 18:42:48 +00:00
ebanks 89771fef05 -Use read.getReadGroup() 
-Add another filter for read groups for Chris


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1835 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 18:08:32 +00:00
ebanks 311ab8da5a A helper class to create the masks for the sequenom design maker. 
This project is now officially done.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1834 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 17:28:51 +00:00
hanna 3553fc9ec0 Preparing for human -- support bwa output files directly rather than relying on a custom fixed sa interval. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1833 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 17:17:46 +00:00
ebanks d89bc2c796 This class no longer outputs in sequenom format 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1832 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 17:16:36 +00:00
ebanks 0c95d6906f Merge both versions of the Sequenom assay design maker: use Jared's base code and add in indels. [Jared, this still emits the same output for SNPs as your original version) 
Remove all sequenom stuff from the FastaAlternateReferenceMaker so it can just concentrate on making alternate references...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1831 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 17:11:45 +00:00
ebanks 49af5269e5 Jared: feel free to change or revert, but until we move over to UG version... 
Only print out positions with at least one non-ref call


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1830 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 17:08:57 +00:00
chartl f5a2e6dd50 Fix! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1829 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 16:15:20 +00:00
ebanks f2886d88e0 We now emit genotype calls 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1828 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 02:49:56 +00:00
ebanks 1b214c0de5 Fixed logic: throw exception if contigs are NOT equal 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1827 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 02:48:44 +00:00
ebanks aeca14d052 On our side of 5CC, we spell multi M-U-L-T-I. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1826 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 01:41:25 +00:00
ebanks c9c8fd1fef Added the discovery LOD score to the meta data 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1825 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-14 01:24:06 +00:00
ebanks 0c06bf9dbc Explicitly set output to GELI now that default is VCF 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1824 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 22:12:03 +00:00
hanna a76fac4687 Cleanup existing speedups. Minor performance improvements. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1823 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 21:51:18 +00:00
hanna 837ae1d33a Optimization: from 22k reads/min - 30k reads/min. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1822 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 20:59:29 +00:00
ebanks 96b8499a31 Remodeled version of the UnifiedGenotyper. 
We currently get identical lods and slods as MultiSampleCaller (except slods for ref calls, as I discussed with Jared) and are a bit faster in my few test cases.  Single-sample mode still emulates SSG.
The remaining to do items:
1. more testing still needed
2. we currently only output lods/slods, but I need to emit actual calls
3. stubs are in place for Mark's proposed version of the EM calculation and now I need to add the actual code.
More check-ins coming soon...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1821 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 20:27:01 +00:00
ebanks b28446acac Multi-sample calls now have associated meta-data (SLOD, allele freq), which wil 
l soon actually be used...


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1820 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 20:08:43 +00:00
hanna db642fd08b Optimization: from 10k reads/sec - 22k reads/sec.. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1819 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 18:07:15 +00:00
aaron 77499e35ac fixes for GSA-199: Need easier way to write binary outputs to standard output. GLF and VCF now have stream constructors, and can get dumped to standard out. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1818 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 15:50:20 +00:00
hanna f37564e63a Our BWA is now looking at roughly the same number of candidate alignments as BWA/C. Performance is now at 11k reads / min, still a long way from BWA/C. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1817 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 15:50:04 +00:00
chartl 8d0e057d83 I got bored today and decided to write the confusion matrix calculator. At present it is untested. I'm submitting it to subversion to make sure 
I have  previous revision to revert back to.


This is a calculator that will calculate:

P[ True base is X | read base mismatches, secondary base is Y, previous K bases are Z1,Z2,...ZK ]

where the number of pervious reference bases to take into account is user-defined. The secondary base is optional as well.

--usePreviousBases k

tells the walker to use the k previous reference bases in the transition table

--useSecondaryBase

tells the walker to use the secondary base at a locus in the transition table

these can be used together.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1816 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 02:55:29 +00:00
ebanks be92a1e603 Don't try to close if the lazy initialize hasn't triggered 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1815 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-13 01:20:25 +00:00
chartl ec83bc6ec5 This somehow didn't make it into subversion the last time. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1814 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-12 21:11:13 +00:00
chartl ecbb11e017 Modified PowerBelowFrequency to ignore reads below a user-defined mapping quality. Request from Jason Flannick. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1813 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-12 20:59:24 +00:00
chartl ec68ae3bc5 Added a filter that will split the read set by a threshold of mapping quality (Request from Jason Flannick) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1812 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-12 20:58:37 +00:00
chartl 0d73fe69e7 Recalibrator by NQS. Had this puppy running all afternoon. Thing had got through 100,000,000 reads before I decided to delete my sting tree. *sigh*, a little more delay. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1811 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-12 20:55:02 +00:00
chartl ee0afba0af Recalibration stuff... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1810 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-12 20:51:39 +00:00
ebanks caf689821f added method to get normalized posteriors 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1809 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-12 02:33:22 +00:00
ebanks cf7a26759d -use the getReadGroup() function that was added to picard for us 
-clean up some include lines


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1808 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-12 01:39:32 +00:00
hanna d844d1c496 SAMFileWriters specified as command-line arguments were sometimes incorrectly altering the default short name. Make sure short name is not specified if shortName is not specified but fullName is. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1807 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-09 19:16:46 +00:00
hanna da084357db Fixed minor typo in output message. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1806 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-09 18:56:54 +00:00
aaron 62c484b57a Fixes for GSA-201, where enumerated types in command line arguments had to be defined as all uppercase for the system to work. 
Also a little playground walker that changes the sort order flag of a BAM file.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1805 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-09 18:11:32 +00:00
hanna 32d55eb2ff Fix issue Eric was seeing with java.lang.Error in unmap0. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1804 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-09 17:46:56 +00:00
ebanks 9f3482ef11 VCF is both a multi- and single- sample format, so we shouldn't be throwing an exception when used for SS 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1803 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-09 17:43:26 +00:00
jmaguire d9f5a314ac avoid an out of memory error by no putting more than 5000 reads in the cache. on pilot1 at least those are crazy loci anyway. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1802 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-09 14:56:55 +00:00
hanna f4b6afb42c JVM issue id 5092131 (http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5092131) 
was causing OOM issues with the new mmapping fasta file reader during large jobs.
Temporarily reverting the reader until a workaround can be found.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1801 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-09 04:45:46 +00:00
chartl 6d7f4481e4 Changed traversal type slightly 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1800 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-09 04:11:48 +00:00
ebanks a9f3d46fa8 Your time has come, SSG. 
Fare thee well.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1799 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 20:27:56 +00:00
jmaguire 8fdb8922b8 now output in the exact format that works with sequenom software. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1798 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 20:06:27 +00:00
aaron 98e3a0bf1a VCF can now be emitted from SSG. The basic's are there (the genotype, read depth, our error estimate), but more fields need to be added for each record as nessasary. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1797 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 19:50:04 +00:00
hanna 95f24d671d Fixed 'visualization' of reads that didn't match bwa's alignments exactly. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1796 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 19:45:30 +00:00
kiran 29ad6cd876 Made redundant by BCMMarkDupes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1795 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 18:47:20 +00:00
kiran 94d82d1915 Matthew Bainbridge's duplicate removal utility for 454 data. This code should eventually be moved into a read walker. For now, it's being introduced into the repository as-is (well, with one minor change to make the handling of command-line arguments a little more straightforward). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1794 348d0f76-0448-11de-a6fe-93d51630548a
 2009-10-08 18:32:37 +00:00