7ce0df76f8
Added accessors to the rod data sources so that walkers can access the name/file/type triplets for input rods. This is necessary if e.g. you want to create a vcf writer based on all of the samples being input.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1994 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 04:25:39 +00:00
d07f3bb6f6
Added methods to get strand bias and to test if record has allele freq or bias fields set.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1993 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-09 04:20:35 +00:00
3313b0ddb4
Fixed a minor bug where the lodThreshold wasn't being printed in the header.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1992 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-08 16:51:36 +00:00
95d381efe2
Optionally computes the error rate using the best base and a random base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1991 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-08 16:47:34 +00:00
567f5758d2
Optionally lists read depths by read group.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1990 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-08 16:39:19 +00:00
a679bdde18
FindContaminatingReadGroupsWalker lists read groups in a single-sample BAM file that appear to be contaminants by searching for evidence of systematic underperformance at likely homozygous-variant sites.
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Procedure:
1. Sites that are likely homozygous-variant but are called as heterozygous are identified.
2. For each site and read group, we compute the proportion of bases in the pileup supporting an alternate allele.
3. A one-sample, left-tailed t-test is performed with the null hypothesis being that the alternate allele distribution has a mean of 0.95 and the alternate hypothesis being that the true mean is statistically significantly less than expected (pValue < 1e-9).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1989 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-08 16:36:39 +00:00
2225d8176e
A convenience class for maintaining a dynamically growing table of values with access to the elements by named row and column identifiers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1988 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-08 16:34:35 +00:00
21c5f543fa
Fix sharding bug -- loci to which >100,000 (= 1 shard) reads are assigned an
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alignment start will confuse the sharding system and cause it to return duplicate reads.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1987 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-08 14:27:26 +00:00
84ba604611
Sequential quality score calculation is now in place in the refactored recalibrator and matches the quality scores calculated by the old recalibrator exactly; at least on the small sets of data used so far. Validation, documentation, and optimization work is on going.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1985 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-07 15:55:16 +00:00
bf1bc94060
Fixes for PooledConcordance bugs and lack of safety checking
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1984 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-07 01:54:10 +00:00
66d4a995e6
Initial check in of refactored Recalibrator. The new walkers are called CountCovariatesRefactored and TableRecalibrationRefactored. More work is needed to finish up the sequential calculation and to document the code sufficiently. These files are not ready to be used by other people quite yet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1982 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-06 22:33:55 +00:00
6fdfc97db6
Added optional field DP to VCF output for Mark.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1981 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-06 20:03:22 +00:00
0a55fa5bb1
Completely refactored the Genotype Concordance module(s).
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Now PooledConcordance and GenotypeConcordance inherit from the same super class (and can therefore share data structures and functionality). Also, they now use ConcordanceTruthTable to keep track of necessary info.
GenotypeConcordance passes integration tests.
PooledConcordance needs to be finished by Chris.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1979 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-06 16:27:16 +00:00
d549347f25
Refactored GenotypeLikelihoods to use an underlying 4-base model.
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It needs to be modified a bit and then hooked up to a pooled model, but that is now possible.
At this point, there is no difference to the Unified Genotyper.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1978 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-05 21:59:25 +00:00
4d3871c655
don't flush anymore.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1977 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-05 19:11:51 +00:00
aacd72854f
a fix for a bug Andrey discovered: in read-based interval traversals we're dupplicating reads in rare cases. The problem was that to accomidate a bug in SAM JDK indexing, we were forced to add one to the stop of our QueryOverlapping() calls to ensure we always got all of the overlapping reads.
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Added a PlusOneFixIterator that wraps other iterators, and eliminates reads that start outside of our intended interval (interval stop - 1). Updated and checked BamToFastqIntegrationTest MD5 sums.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1976 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-05 05:26:33 +00:00
43c3ee61d5
Fix minor mapping quality bug.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1973 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-04 14:33:23 +00:00
a545859c62
Joint Estimation model now emits a reasonable slod
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1969 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 21:12:42 +00:00
11d950abe0
No longer allow the lod_threshold argument - use confidence instead.
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Have UG output qscores in all cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1968 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 16:18:51 +00:00
2fb45dbd73
Make window size a command line argument
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1967 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 16:13:35 +00:00
55f61b1f88
Bug fix in adjustment of the shift position.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1966 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 16:08:11 +00:00
5d5dc989e7
improvements to VCF and variant eval support of VCF -- now listens to the filter field
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1963 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 12:09:30 +00:00
c63af32fc7
The BWA/C bindings were triggering the local aligner to repeatedly reload the
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ref genome. Make sure the reference genome is cached.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1961 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 00:01:55 +00:00
3a33401822
2nd stage of the genotyper output refactoring is complete.
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Now, all output is generalized and all of the intelligence lies where it is supposed to.
Next stage is syncing up old and new models and making sure we're outputting exactly what we should.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1960 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-02 22:43:08 +00:00
ba67c7f02b
added a warning for those using bed files; we properly convert bed to the internal representation but the user needs to be aware that any output will be one-based closed intervals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1959 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-02 21:09:18 +00:00
b71b66bd88
the underlying parameter is a float so we need to use Float.valueOf() instead; Noticed by external user Hou Huabin
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1958 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-02 20:22:25 +00:00
5a510e6d98
New PackageUtils interferes with the packaging utility. Revert until Aaron and
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I can get together to make this work.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1957 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-02 19:14:14 +00:00
de6ae51f7e
Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar.
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A couple of notes:
-Commented out BaseTransitionTableCalculator.scala because it's won't build; Chris could you fix this one (or kill it if it's not needed).
-Removed the PrintReadsScala walker; moved the code over to a ScalaCountLoci walker (which is what the code was really doing).
-Added configurations items to the ivy xml file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1956 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-02 06:02:41 +00:00
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
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.
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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
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.
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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
55fa1cfa06
-Renamed new calculation model and worked out some significant xhanges with Mark
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-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
8e3f72ced9
BTTJ - Code refactoring (major) - passes integration test
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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
15a1849758
notes for chartl
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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
77863d4940
@PowerBelowFrequency
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+ 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
967128035e
Make command like args default to false.
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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
9b9744109c
Mark's new unified calculation model is now officially implemented.
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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
caa3187af8
Enabling correct high-performance ROD walker and moved VariantEval over to it. Performance improvements in variantEval in general. See wiki for full description
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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
4a8a6468be
Use read group as a condition for confusion tables. With an integration test.
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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
b83df5616a
Change for lower-case references (always compare upper case bases)
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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
3b1fabeff0
Major code refactoring:
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@ 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
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.
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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
449a6ba75a
Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered.
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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
d749a5eb5f
added a check to ensure the eval track variation is bi-allelic. Also changed some string constants over to enums
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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
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).
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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
a8a2c1a2a1
Replaced SSG with UG in packaging utils. Minor performance and formatting improvements for ClipReads
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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
c29924e7cf
Reverting previous change.
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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
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
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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
761a730758
assertBiAllelic -> assertMultiAllelic.
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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
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.
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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
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.
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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
10bde9e77b
Integration test for BTT calculator
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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
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
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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
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.
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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
225ef52973
Now produces same output as the Scala walker for unconditioned tables (no 2bb, no previous base, etc.)
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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
bb180a23ef
Updated MD5
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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
51f9ec0a5c
subtract largest posterior value from all values; this hopefully solves any precision issues
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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
b9e8867287
-push allele frequency and genotype likelihood variable definitions down into the subclasses so that they can use different data structures
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-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
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.
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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
ad777a9c14
@BasicPileup - made the counts public so they can be used
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@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
bdb34fcf38
Updated integration tests for VariantEval. Hooray for IT!
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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
41a95cb3f0
fixing unified genotyper test for change: VCF output now emits no calls as ./.
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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
85a4fbc256
Bumping version of Picard for firehose compatibility.
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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
8aacc43203
VCF output now emits no calls as ./.
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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
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".
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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
07b134a124
Added some integration tests for multiple samples
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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
418e007ca6
A cleaner interface: now everyone can use UG's initialize method
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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
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.
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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
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.
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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
b82c3b6040
Better error output (and fixed spelling mistakes)
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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
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.
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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
7d7ff09f54
throw an exception if read has no associated read group
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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
b9544d3f89
Output formatting change (very slight)
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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
839c5d66bc
Read uints directly into longs.
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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
ce38fa7c81
Breaking the signed int glass ceiling; stage 1: convert critical ints to longs. Code cleanup and documentation.
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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
79993be46c
changed blank gene name to UNKNOWN
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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
0c2016c19a
Improved error messages -- now easier to read, points to the GATK Error Messages wiki, and avoids double printing of stack traces
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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
a9094c835c
clean-up and fixes to the VCF input
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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
a32470cea1
Deal with the fact that walkers can call UG's init/map functions directly.
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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
8dca236958
Base-packed reader cleanup.
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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
316b30ee56
On the road to human: make sure the suffix array will fit in a Java array.
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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
e740e7a7ce
Because walkers call UG's map function, we need to move the actual writing out
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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
825e6c7a4d
added calculation for bases over 2x,10x,20x,30x plus gene name
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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
727b69fce0
catch null output destinations earlier
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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
1f66738c8e
Fix a hashing function bug. Ignore reads with non-reference bases in the pileup.
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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
72c34f11dd
Bug fixing for BWA output formats.
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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
60183229ab
the oldest java mistake in the book...
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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
52d2e0ca07
All walkers now use read.getReadGroup()
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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
0a09fa4d5c
Rename to distinguish this transition table calculator from the scala version.
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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
1d055011bd
Getting rid of this so I can rename it without the world blowing up.
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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
eb90e5c4d7
changes to VCF output, and updated MD5's in the integration tests
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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
89771fef05
-Use read.getReadGroup()
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-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
311ab8da5a
A helper class to create the masks for the sequenom design maker.
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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
3553fc9ec0
Preparing for human -- support bwa output files directly rather than relying on a custom fixed sa interval.
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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
d89bc2c796
This class no longer outputs in sequenom format
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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
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)
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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
49af5269e5
Jared: feel free to change or revert, but until we move over to UG version...
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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
f5a2e6dd50
Fix!
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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
f2886d88e0
We now emit genotype calls
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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
1b214c0de5
Fixed logic: throw exception if contigs are NOT equal
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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
aeca14d052
On our side of 5CC, we spell multi M-U-L-T-I.
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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
c9c8fd1fef
Added the discovery LOD score to the meta data
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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
0c06bf9dbc
Explicitly set output to GELI now that default is VCF
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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
a76fac4687
Cleanup existing speedups. Minor performance improvements.
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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
837ae1d33a
Optimization: from 22k reads/min - 30k reads/min.
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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
96b8499a31
Remodeled version of the UnifiedGenotyper.
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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
b28446acac
Multi-sample calls now have associated meta-data (SLOD, allele freq), which wil
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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
db642fd08b
Optimization: from 10k reads/sec - 22k reads/sec..
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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
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.
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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
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.
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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
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
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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
be92a1e603
Don't try to close if the lazy initialize hasn't triggered
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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
ec83bc6ec5
This somehow didn't make it into subversion the last time.
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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
ecbb11e017
Modified PowerBelowFrequency to ignore reads below a user-defined mapping quality. Request from Jason Flannick.
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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
ec68ae3bc5
Added a filter that will split the read set by a threshold of mapping quality (Request from Jason Flannick)
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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
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.
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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
ee0afba0af
Recalibration stuff...
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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
caf689821f
added method to get normalized posteriors
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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
cf7a26759d
-use the getReadGroup() function that was added to picard for us
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-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
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.
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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
da084357db
Fixed minor typo in output message.
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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
62c484b57a
Fixes for GSA-201, where enumerated types in command line arguments had to be defined as all uppercase for the system to work.
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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
32d55eb2ff
Fix issue Eric was seeing with java.lang.Error in unmap0.
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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
9f3482ef11
VCF is both a multi- and single- sample format, so we shouldn't be throwing an exception when used for SS
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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
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.
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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
f4b6afb42c
JVM issue id 5092131 ( http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5092131 )
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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
6d7f4481e4
Changed traversal type slightly
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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
a9f3d46fa8
Your time has come, SSG.
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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
8fdb8922b8
now output in the exact format that works with sequenom software.
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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
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.
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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
95f24d671d
Fixed 'visualization' of reads that didn't match bwa's alignments exactly.
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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
29ad6cd876
Made redundant by BCMMarkDupes
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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
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).
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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
15bf014e0b
logger.info -> logger.debug (don't want to risk filling up my log on genome-wide calls)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1792 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 17:53:11 +00:00
df8ea8f437
UG integration test. This was the old SSG test with MD5s updated.
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I'll need to add some multi-sample tests in a bit...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1791 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 17:43:58 +00:00
008455915a
One way of making the integration test stop failing is to remove it...
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[waiting for Matt to cringe...]
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1789 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 17:08:41 +00:00
f89a89ffe3
Use of AlleleFrequency as an input to PowerAndCoverage is deprecated by the new walker. Reverting to the standard "power at 1 allele" calculation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1788 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 16:07:45 +00:00
ae05f5c7ad
Fixin the header.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1787 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 15:49:28 +00:00
11ff1e09b8
A new power walker for the user to feed in a number of alleles. Call that number k. Output is:
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Locus Power_for_k_alleles Power_for_k-2_alleles Power_for_k-2_alleles ... Power_for_1_allele
This was a request from Jason Flannick & the T2DB group.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1786 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 15:35:35 +00:00
04fe50cadd
*** We no longer have a separate model for the single-sample case. ***
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For now, a single sample input will be special-cased in the EM model - but that will change when the EM model degenerates to the single sample output with a single sample as input. For now, the EM code for multi-samples isn't finished; I'm planning on checking that in soon.
The SingleSampleIntegrationTest now uses the UnifiedCaller instead of SSG, and so should all of you. More on that in a separate email.
Other minor cleanups added too.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1785 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 14:08:57 +00:00
32128e093a
misc. changes to get the numbers back to the baseline while keeping the speedup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1784 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 12:27:07 +00:00
d38a0d04b9
fix a snp mask offset error.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1783 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 12:25:40 +00:00
829e99413b
Rescores a variant after removing duplicates (defined very strictly as reads with the same start points).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1782 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 03:07:36 +00:00
fcb6a992c8
Switched IndexedFastaSequenceFile over to use memory mapping to load data rather than
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the loop-with-small block size. Performance improvements in loading refs are extreme;
segments can be loaded in <1ms. chr1 in its entirety can be loaded in 1.5sec (down
from 30sec).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1781 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-08 00:07:15 +00:00
02d2492d68
Simple tool for picking sequenom probes for SNPs. Can be extended to indels if necessary.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1780 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-07 23:46:41 +00:00
1905b5defa
Hash by chromosome for now to reduce memory. This is a temporary solution until we decide how to reture the Injector for good.
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Also, with Picard's latest changes, we need to make sure we don't double-close the sam writer.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1779 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-07 20:06:25 +00:00
f9a1598d75
Reformatting
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1778 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-07 20:03:34 +00:00
203c626fc2
A wrapper around the GenotypeLikelihoods class for the UnifiedGenotyper. This wrapper incorporates both strand-based likelihoods and a combined likelihoods over both strands.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1777 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-07 19:57:37 +00:00
5bdcc2b4dc
Included HLA class 2 genes in CreatePedFileWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1776 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-07 18:46:51 +00:00
8f896b734f
Included HLA class 2 genes in CreatePedFileWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1775 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-07 18:28:01 +00:00
f9a0eefe4b
GELI_BINARY is now functional, and can be used as a variant type in SSG (-vf=GELI_BINARY). Also fixed the max mapping quality column in both GELI output formats, we haven't been correctly outputing up until now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1774 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-07 18:20:34 +00:00
225b9bccc1
Modifications to NQSClusteredZScoreWalker to output empirical mismatch rates on bins by both Z-score and reported Q-score, rather than averaging over all Q-score bins for each Z-score.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1773 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-07 13:45:12 +00:00
8dd0924b37
Minor performance improvements to VariantEval -- now all of the CPU time is spent dealing with the ROD system...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1772 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-06 23:40:30 +00:00
4554ca1b28
more cleanup, depecaited the old genotype, corrected SNPCallsFromGenotypes' imports and two other classes that depend on it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1771 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-06 19:09:27 +00:00
3aec76136f
Removing the AllelicVariant interface, which is replaced by the Variation interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1770 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-06 17:44:24 +00:00
1bd0c3c145
variant eval allows non Variation rod objects
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1768 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-06 13:04:26 +00:00
66fc8ea444
GSA-182: Adding support for BED interval files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1767 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-06 02:45:31 +00:00
aec83b401d
SSG multithreading doesn't play well with some I/O changes made since I last svn up'd. Reverting until I can find the reason.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1766 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-05 19:48:57 +00:00
8a503c86b6
Code supporting SSG proof-of-concept shared memory parallelism.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1765 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-05 18:56:16 +00:00
fb619bd593
-Refactoring: make GenotypeCalculationModel constructors empty so that they don't have to be updated every time we add a new parameter; instead put that logic in the super class's initialize method (making everything protected so that only the factory can access them)
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-Adding initial version of Multi-sample calculation model. This still needs much work: it needs to be cleaned up and finished. Right now, it (purposely) throws a RuntimeException after completing the EM loop.
Also:
-Fix logic in GenotypeLikelihoods.setPriors
-Add logger to the models for output
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1764 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-05 18:10:36 +00:00
98076db6b4
Modified CreatePedFileWalker to output PED file given HLA allele names
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1763 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-05 03:06:42 +00:00
56bc4fa21a
Fixed bug where not all alignments were returned if read aligned to multiple locations. Enhanced test suite to validate all alignments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1762 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-04 18:20:20 +00:00
05aa928e3e
Fix off-by-number-of-deletions issue with negative strand reads. Improved performance by factor of 2.5x.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1761 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-03 21:55:18 +00:00
7605ee500c
Idiocy! All tests were being disabled because I forgot the instanceof
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1760 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-02 20:04:56 +00:00
88d0890cc3
Made PooledGenotypeConcordance a standard test in VariantEval
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1759 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-02 20:03:31 +00:00
7fc4472e6d
A big fix for MergingSamRecordIterator, where we weren't correctly handling the comparisons of SAMRecords correctly (we weren't applying the new reference index first, so sometimes the MT contig would be ID 23, sometimes 24 in different records).
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Also a fix to the GLF tests, and a correction to PrintReadsWalker to remove the close() on the output source, the source handles that itself (and you get a double close).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1758 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-02 19:35:35 +00:00
68cb2ee54b
Tweaks to parameters for NQS analysis walkers; change to PowerAndCoverage for Jason Flannick (can input the number of alleles to compute power for - i.e. doubletons, tripletons; rather than statically checking singletons.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1757 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-02 19:11:27 +00:00
7249fade05
updated
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1756 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-02 18:10:34 +00:00
53a4bd7f51
A better understanding of what's going on means no need for clearing the cache
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1755 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-02 18:07:46 +00:00
e885cc4b21
changes for corrected GLF likelihood output, along with better tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1754 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-01 20:45:05 +00:00
2309d19f6f
Bug fix from Michael Ross: mark second read in sequence as second of pair.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1753 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-01 14:34:36 +00:00
2e4949c4d6
Rev'ing Picard, which includes the update to get all the reads in the query region (GSA-173). With it come a bunch of fixes, including retiring the FourBaseRecaller code, and updated md5 for some walker tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1751 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-30 20:37:59 +00:00
303972aa4b
Yup, I broke the build...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1750 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-30 20:20:43 +00:00
841d25cc44
Added ability to set the priors after construction (and requiring a flushing of the likelihoods cache)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1749 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-30 19:55:49 +00:00
665951f9f0
Support negative strand alignments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1748 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-30 18:10:26 +00:00
d3b1732cca
Start of refactoring effort. Make construction of alignment object simpler.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1747 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-30 15:19:31 +00:00
70e1aef550
Better integrate the @ArgumentCollection into the command-line argument parser. Walkers can now specify their own @ArgumentCollections. Also cleaned up a bit of the CommandLineProgram template method pattern to minimize duplicate code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1746 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-29 22:23:19 +00:00
b1c321f161
Adjusted Genotype concordance to more accurately use the new Genotyping code, fixed the VCF rod, and temp. fix the build by reintroducing Shermans ReadCigarFormatter
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1745 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-29 21:28:21 +00:00
9b78a789e2
HLA Caller 2.0 Walkers:
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CalculateBaseLikelihoodsWalker.java walks through reads calculates likelihoods using SSG at each base position
CalculateAlleleLikelihoodsWalker.java walks through HLA dictionary and calculates likelihoods for allele pairs given output of CalculateBaseLikelihoodsWalker.java
CalculatePhaseLikelihoodsWalker.java walks through reads and calculates likelihoods score for allele pairs given phase information
File Readers:
BaseLikelihoodsFileReader.java reads text file of likelihoods outputted by SSG
FrequencyFileReader.java reads text file of HLA allele frequencies
PolymorphicSitesFileReader.java reads text file of polymorphic sites in the HLA dictionary
SAMFileReader.java reads a sam file (used to read HLA dictionary when in another walker)
SimilarityFileReader.java reads a text file of how similar each read is to the closest HLA allele (used to filter misaligned reads)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1744 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-29 20:45:55 +00:00
281a77c981
Bugfix. isMismatch() was actually computing isMatch().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1743 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-29 20:04:59 +00:00
e28b45688c
More NQS Related Walkers to play with
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1742 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-29 20:01:04 +00:00
9ef80e3c3c
One minor addition: to incorporate Pooled calling (and to be as general as possible), we allow the genotype calculation model to use rods if it wants.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1741 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-29 17:05:59 +00:00
19bfe43173
First pass at a unified caller, being checked in now so Mark can give feedback if he chooses and so Matt can debug issues with the ArgumentCollection class.
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Some notes:
1. This design should be flexible enough to include pooled calling (for now) after discussions with Chris.
2. Using the unified caller with the SingleSampleCalculationModel emits the exact same output as SSG over all of chr20 for NA12878. Additionally, when we include the "max deletions allowed at a locus" argument (so we don't try to call SNPs at deletion sites), it removed 233 SNP calls in chr20 that were clearly indel artficts.
3. The MultiSampleEMCalculationModel is still a work in progress and will be checked in later this week.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1740 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-29 16:48:15 +00:00
8bd345ba00
Generalized deletions in pileup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1739 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-29 15:58:43 +00:00
6134f49e3c
Convert de novo SNP caller to run using parent1 and parent2 BAM files (by splitting contexts by reader using getMergedReadGroupsByReaders) instead of geli files providing a large speed-up and obviating the need for large whole-genome geli files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1738 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-29 06:42:21 +00:00
5dab95aa5a
Fix getMergedReadGroupsByReaders so that it provides read groups in the same way Picard does so that it works correctly when input read files have no clashes in their read groups and retain their original read group names.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1737 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-29 06:35:50 +00:00
5662a88ee1
Cosmetic change to list sampling functions: the typical usage of n and k were reversed. No change in functionality of the classes has been made and unit tests still pass.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1736 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-28 18:12:32 +00:00
39598f1f0a
switching the concordance walker over to the new Variation system
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1735 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-28 15:46:36 +00:00
bce2f0d7cf
Now instantiates the list of alternative consenses to evaluate as LinkedHashSet to guarantee iterator traversal order. Old implementation used HashSet and exhibited unstable behavior when two alt consenses turned out to be equally good: depending on the run conditions (including size of the interval set being cleaned??), either one could be seen first as selected as the 'best' one
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1734 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-28 06:15:46 +00:00
663175e868
Bug fix: when jumping onto next contig (chromosome), the walker was erasing last mismatch interval from the previous chr it was still holding without printing it; now it gets printed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1733 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-25 22:24:34 +00:00
92c6efabb7
moving IndelGenotyper out of playground
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1732 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-25 19:44:49 +00:00
aec61c558b
moving IndelGenotyper out from playground
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1731 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-25 19:43:53 +00:00
fe6d810515
Some basic commits that I've been sitting on for a while now:
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@ PooledGenotypeConcordance - changes to output, now also reports false-negatives and false-positives as interesting sites. It's been like this in my directory for ages, just never committed.
@NQSExtendedGroupsCovariantWalker - change for formatting.
@NQSTabularDistributionWalker - breaks out the full (window_size)-dimensional empirical error rate distribution by the window. So if you've got a window of size 3; the quality score sequences 22 25 23 and 22 25 24 have their own bins (each of the 40^3 sequences get one) for match and mismatch counts.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1730 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-25 19:35:50 +00:00
f7684d9e1b
ImputeAllelesWalker fills missing portions of HLA dictionary based on best allele matches
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1729 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-25 18:51:46 +00:00
235de38c2e
Updates to FindClosestAlleleWalker and CreateHaplotypesWalker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1728 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-25 16:41:58 +00:00
130a01a40a
delete the integration test temp files when the test is over
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1727 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-25 16:34:08 +00:00
2b7d39035a
switched over the FastaAlternateReferenceWalker to the Variation system
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1726 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-25 16:09:43 +00:00
7ffc1d97ef
Cut DeNovoSNPWalker over to the new Variation system, some renaming of methods on the Variation interface, and some corrections on the interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1724 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-25 04:35:52 +00:00
392152f149
1000x performance improvements to MSG for crisis control
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1723 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-24 23:44:33 +00:00
44879c81b0
Add in weights. Massive performance improvements.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1722 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-24 23:19:15 +00:00
3b79f9eddc
Support 'N's and other mismatch characters in the reference.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1721 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-24 21:41:30 +00:00
ebanks
kiran
hanna
rpoplin
depristo
jmaguire
aaron
asivache
chartl
sjia
andrewk
kcibul