58b2578c44
Several changes to CovariateCounter walker to print more tables (called vs. observed Q scores), bug fixes to LogisticRecalibrationWalker and LogisticRegressor, and print string functionality added to Pair.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@550 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-28 00:37:48 +00:00
a0a581171b
print out the last interval
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@549 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-27 20:43:06 +00:00
a343f3eab7
Fixed bug where we weren't setting the reads group correctly. Also added code to set the printMetrics field of the singleSampleGenotyper from the Pool caller, it was null excepting out for me without that set.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@548 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-27 15:17:20 +00:00
1daf8e0987
A utility to compare the results of the SingleSampleGenotyper in 1-base and 4-base mode.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@547 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-27 15:10:08 +00:00
444bc18183
Removed binomialProb() method. Set better values for qHom, qHet, and qHomNonRef and allowed those to be set from the command-line.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@546 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-27 15:09:02 +00:00
b9c9dbb1d7
Added multinomialProbability method.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@545 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-27 15:03:50 +00:00
eeb0b78cce
Added another assert to testBinomialProbability() and added a test method for testMultinomialProbability().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@544 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-27 14:59:11 +00:00
9a8902571c
Placeholder for parallel MicroManager.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@542 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-26 23:08:12 +00:00
1daa011387
Interval-based traversals were bleeding file handles. Fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@541 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-26 18:35:54 +00:00
1e2e78265d
Inadvertently removed interval file support in new TbLbR. Fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@540 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-26 18:15:42 +00:00
c9e9731495
More cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@539 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-26 17:46:52 +00:00
4036f24909
Documentation and cleanup work in preparation for parallelism.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@538 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-26 17:42:00 +00:00
0c76a70313
Renamed traversal by "interval" to "locusWindow"
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@537 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-26 02:26:08 +00:00
9a299c11d3
Oops, typo and build problems. FYI, fixing typos is better than packing...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@536 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-25 01:37:17 +00:00
ce470702fc
consistency with java naming conventions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@535 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 21:44:48 +00:00
bfce0c93ab
removing bad file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@534 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 21:40:04 +00:00
05c6679321
Enabled ReduceByInterval
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@533 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 21:39:44 +00:00
ee2f022c71
Make new TraverseByLociByReference the default.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@532 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 19:50:11 +00:00
e50ae97fe1
Introduce new index-based fasta reader. Clean up MicroManager code, pushing necessary code back into TraversalEngine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@531 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 19:40:21 +00:00
40a2b3eeb3
Basic logistic regression support for calibrating qualities; mostly for Andrew to experiment with
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@529 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 19:09:50 +00:00
061f4328b1
Covariate counter now outputs files used by R to do logistic regression.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@527 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 17:11:57 +00:00
4e4fd33584
First draft of actual pooled EM caller.
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Produces sane looking output on region of 1kG pilot1:
CALL NA12813.SRP000031.2009_02.bam CC 0.609084 0.609084
CALL NA12003.SRP000031.2009_02.bam CC 2.114234 2.114234 CCCCC
CALL NA06994.SRP000031.2009_02.bam CC 0.910114 0.910114 C
CALL NA18940.SRP000031.2009_02.bam CT 2.589749 0.910114 T
CALL NA18555.SRP000031.2009_02.bam CC 0.609084 0.609084
Next up, eval vs. Baseline pilot1 calls and pilot3 deep-coverage truth.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@526 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 13:43:41 +00:00
dd408a2a9a
First draft of actual pooled EM caller.
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Produces sane looking output on region of 1kG pilot1:
CALL NA12813.SRP000031.2009_02.bam CC 0.609084 0.609084
CALL NA12003.SRP000031.2009_02.bam CC 2.114234 2.114234 CCCCC
CALL NA06994.SRP000031.2009_02.bam CC 0.910114 0.910114 C
CALL NA18940.SRP000031.2009_02.bam CT 2.589749 0.910114 T
CALL NA18555.SRP000031.2009_02.bam CC 0.609084 0.609084
Next up, eval vs. Baseline pilot1 calls and pilot3 deep-coverage truth.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@525 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 13:42:15 +00:00
13d4692d2e
1. Added a by-interval traversal.
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2. Added a shell for the indel cleaner walker (it's currently being used to test the interval traversal).
3. Fixed small bug in downsampling (make sure to downsample the offsets too)
4. GenomeAnalysisTK.execute => anyone object to my change to "instanceof" instead of trying to catch a ClassCastException (yuck)?
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@524 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 04:33:35 +00:00
1984bb2d13
Made num_loci_total public because I'm lazy. I'll change it back later.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@523 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 03:57:23 +00:00
7ce11e152b
Simplified. Added option to perform four-base retest of a putative variant.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@522 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 03:56:15 +00:00
135d3eabeb
Now only distributes 80% of the residual probability to the secondary base, 10% each to the other two bases. Nicer labelling for stringified probability distribution output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@521 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 03:34:43 +00:00
3cda85f2e3
New implementation of binomial probability that accurately computes values down to around 1e-237.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@520 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 03:32:04 +00:00
305584b69e
Test class for MathUtils with a test for binomialProbability().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@519 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 03:31:02 +00:00
bd4cacb832
Added code to make a read group and sample name for BAM files that don't annotate them on reads. The defaults for both are now the filename, but this may be shortened in the future.
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The sample name for a read can be retrieved with the command:
read.getAttribute(SAMTag.RG.toString());
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@518 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 00:31:00 +00:00
45d962e491
I understood the contig index incorrectly when I initially wrote this code. Fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@517 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 22:31:43 +00:00
635bfd8604
Added a little bit of hack to get the header back to the walker by initialization time, which was before sharding in the last version.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@516 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 21:07:11 +00:00
0208d201c7
Forgot this in the last commit...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@515 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 20:47:22 +00:00
3dc2afd7ab
Added the ability to get a merged header in a LociByReference traversal
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@514 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 20:34:52 +00:00
282f1d88b8
Make the operation 'read from the iterator and place on the queue' atomic with respect to hasNext(), next().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@513 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 20:16:26 +00:00
998763950c
Oops, contig index is a zero not one based value
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@512 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 19:08:16 +00:00
8c13940c5a
A lot of changes to support by-read sharding and some from debugging of the by loci traversals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@511 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 19:03:14 +00:00
32715a6c47
First check-in of walker that produces tables showing covariation of read cycle, and dinucleotide with quality score in a format usable for R analysis and for doing logistic regression.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@510 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 18:58:25 +00:00
0720d248ce
Adding the test case for by reads sharding of BAM data sources
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@509 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 18:01:22 +00:00
cae54ec52d
Walker for creating intervals to be used in the indel cleaner
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@508 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:58:19 +00:00
96db1477d4
I meant for default lod threshold to be 5.0, not 0.0.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@507 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:46:08 +00:00
ca66cccd2f
Privatized constructor to prevent instantiation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@506 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:45:39 +00:00
77e1e9e2f1
Added a static class to house useful math methods. All this has at the moment are methods for comparing doubles and floats, but I suggest that the bulk of our little math methods should be added here to avoid filling up Utils.java with so much random stuff.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@505 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:45:19 +00:00
3d7575bbb8
Oops...omitted walker.initialize().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@504 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:35:28 +00:00
11e85f1969
Four-base mode now estimates the genotype using the one-base method and retests the site if the one-base method suggests the site is a het.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@503 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:23:24 +00:00
bd719f9c06
When checking that values are not infinite, also prints out the position so that I know which site was giving the error and I can just go there and debug it.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@502 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:21:58 +00:00
efba30f1a1
Added a constructor in which the lod threshold can be set.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@501 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 17:20:48 +00:00
8c1905c7d9
Simple walker to print all of the sample names present in a merged bam file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@500 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-23 12:26:56 +00:00
a3a1c9dae8
Suppressed emission of duplicate paths through a four-base pileup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@498 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 21:08:45 +00:00
6cef8bd76c
added k-best quality path enumeration.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@497 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 20:26:51 +00:00
d99d67d51c
Refactored to clean it up a bit
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@495 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 19:18:46 +00:00
1bf4d040d8
Increase default shard size from 5 to 100000.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@494 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 18:29:44 +00:00
3af66a462e
Make PrintLocusContextWalker less verbose.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@493 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 18:28:02 +00:00
ffcd672c1c
Intermediate commit while working on getting four-base probs to work in the single sample genotyper. Has infrastructure for the new combinatorial approach and just choosing the best base more intelligently given a probability distribution over bases and the reference base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@492 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 18:06:50 +00:00
4cafb95be8
TraverseByLoci / TraverseByLociByReference suffered from the same sam-triggered off-by-one (?) bug as TraverseByReference; it was just less obvious here because these versions don't shard.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@491 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 15:48:20 +00:00
cb2f621d01
reverting accidental commit of change to shard size
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@490 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 00:33:28 +00:00
b820130dce
* added ability to load multiple BAM files from command line
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@489 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 00:28:08 +00:00
5b8502745a
Added an epsilon (1e-4) to the tertiary and quaternary base hypotheses.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@488 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-22 00:01:37 +00:00
2ac240d78b
Removed an extraneous print statement.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@487 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 23:36:36 +00:00
0149c887ff
Fixed a bug wherein the residual probability was not being distributed properly when a file had secondary probs and the best and next-best base agreed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@486 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 23:36:09 +00:00
5abfc7d079
Added an argument ('extended' or 'ext') that outputs the four-base probs in a long format.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@485 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 22:27:26 +00:00
dac76f041b
Added some methods to retreive the probability distributions of individual bases.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@484 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 22:26:25 +00:00
5b2a7c9c23
Added some methods to complement a single simple base ([AaCcGgTt]) and reverse-complement a byte-array of bases.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@483 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 22:25:33 +00:00
521e202a10
updated interface
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@482 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 21:07:20 +00:00
55ca272919
reimplemented; now implements Genotype interface instead of AllelicVariant
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@481 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 21:06:42 +00:00
5f37ba8f26
now can be asked to log at INFO level all concordant or discordant sites, or both
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@480 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 21:03:44 +00:00
1f84b9647d
auxiliary data structure for mendelian concordance reporting; it's nice to have the latest version checked in in order for the code to compile...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@479 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 21:02:40 +00:00
ece3e9969e
one trivial walker to filter reads; bam in -> filter -> bam out
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@478 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 20:39:29 +00:00
61e855200d
latest version...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@477 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 20:38:37 +00:00
64b2fd866f
* extracted core quality-score based genotype likelihood code
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* precompute expensive operations (log/pow) based on Picard experience
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@476 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 18:58:43 +00:00
11c520b283
completed my old draft of the old school single sample genotype walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@475 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-21 05:38:04 +00:00
b8233d92c8
Simple IO walker to test / crush file systems and evalute I/O performance in general
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@474 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-20 14:07:14 +00:00
bf76eab955
whoops; fix a comment line.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@473 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-19 17:54:54 +00:00
bcba1ff424
Fix a minor rounding bug and putz around with fractional counts in the pooled caller.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@472 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-19 17:52:24 +00:00
af6788fa3d
Misc:
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1. Added logGamma function to utils
2. Required asserts to be enabled in the allele caller (run with java -ea)
3. put checks and asserts of NaN and Infinity in AlleleFrequencyEstimate
4. Added option FRACTIONAL_COUNTS to the pooled caller (not working right yet)
AlleleFrequencyWalker:
5. Made FORCE_1BASE_PROBS not static in AlleleFrequencyWalker (an argument should never be static! Jeez.)
6. changed quality_precision to be 1e-4 (Q40)
7. don't adjust by quality_precision unless the qual is actually zero.
8. added more asserts for NaN and Infinity
9. put in a correction for zero probs in P_D_q
10. changed pG to be hardy-weinberg in the presence of an allele frequency prior (duh)
11. rewrote binomialProb() to not overflow on deep coverage
12. rewrote nchoosek() to behave right on deep coverage
13. put in some binomailProb() tests in the main() routine (they come out right when compared with R)
Hunt for loci where 4bp should change things:
14. added FindNonrandomSecondBestBasePiles walker.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@471 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-19 15:35:07 +00:00
eafb4633ba
Temporary workaround for samtools index bug: there seems to be an off-by-one error. Will file bug report.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@470 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 23:14:41 +00:00
758db73b98
Fixed SLOWNESS issue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@469 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 20:10:34 +00:00
2a937fa8d3
set SAM file header's sorting order to unsorted, hopefully it will help to speed things up
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@468 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 19:32:24 +00:00
03ec3452f2
a first, simplest version of a walker that filters out reads based on user-specified criteria and writes remaining reads into a new bam file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@467 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 18:51:39 +00:00
f2f9fa3ed4
doc added
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@464 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 16:43:25 +00:00
d639ec3776
Remove some copied code to make sure the traversal engine stays in sync with the locus context provider.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@463 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 16:41:56 +00:00
df5aae5ed4
got read of a couple of warnings and added percentage(x,base) methods
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@462 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 15:15:21 +00:00
50ae1763f7
Support for -continue_after_errors flag in the validating pileup walker in case you want to see errors as they arise, rather than aborting greedily
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@461 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 03:13:11 +00:00
ee5ab9536f
trivial checking / flagging issues to enable testing of merging iterator performance
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@460 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 03:11:59 +00:00
dbf2344cef
Fixes for including duplicate reads in the locus traversal; now checks that the ref arg is provided when needed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@459 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-17 01:27:36 +00:00
01be8f09e3
Exception cleanup. All our non-runtime exceptions should extend from StingException, StingException needs to be lower in the tree to build.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@457 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 22:17:25 +00:00
e5c80e59dc
fixed the case when you're not seeking, it didn't initalize
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@456 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 22:16:03 +00:00
f47f640df6
Better debugging output and testing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@455 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 21:54:56 +00:00
165e504d1c
Turn on new TraverseLociByReference is now only dependent on the -et flag. REGION_STR does not matter.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@454 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 19:45:47 +00:00
12e1f192c4
Fixed a bug in this code where it would eat reads that didn't start at the beginning of the provided interval. This should fix / help fix Kristian problem
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@453 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 18:42:00 +00:00
835f1067d8
added isHom() and isHet() queries to the Genotype interface (with the obvious meaning)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@452 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 18:41:39 +00:00
55537c0d1e
chnage class name, now it compiles...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@451 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 16:51:00 +00:00
4f9bc7206f
some cleanup, also ensuring that all reads get written into output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@450 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 16:49:25 +00:00
e8a6cdb386
renamed standalone main
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@449 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 15:56:46 +00:00
832afd3d60
renamed standalone main
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@448 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 15:56:27 +00:00
85308f4ddc
resurrected indel tool's standalone main
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@447 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 15:55:52 +00:00
6f56938d42
* added a bit more debugging output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@446 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 15:20:26 +00:00
d35a542bb9
* fixed bug where the merged header was not being set on the read (although the read group was)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@445 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 12:53:07 +00:00
240eb18564
fix a few related issues when not all the reads were written into the output files. now cleaned output still contains all reads either with modified alignments or untouched
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@444 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 03:56:47 +00:00
0d324354ae
separate interface for genotypes as opposed to (population) allelic variants
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@443 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 03:55:16 +00:00
7e05b43f40
* added some error checking for read groups
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@442 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 03:22:49 +00:00
56f6847456
Changed interface from contig,pos,length to more common contig,start,stop interface.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@441 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-16 00:04:41 +00:00
7261787b71
Fixed potential bug with next() operation returning empty contexts when a read contains a large deletion. We can now use the look ahead safely...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@438 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 21:38:28 +00:00
e70aecf518
bug fix, but important
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@437 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 21:07:20 +00:00
76d833e39b
Meaningful assert messages
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@435 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 19:12:28 +00:00
67ea66c866
Bug fix
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@434 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 19:12:18 +00:00
1edfe48194
Better debugging output with .debug
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@433 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 19:09:18 +00:00
9cc808104e
Fixed subtle bug in permitting EXPAND_WINDOW to be > 1. We now use the right window size so we avoid including empty hangers. There's still a rare bug to sort out, which occurs in the case where a read with an indel can generate empty hangers.
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Also cleaned up the debugging output.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@432 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 19:08:26 +00:00
180ff13290
Added a bunch of changes to support the new MicroManager code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@431 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 18:29:38 +00:00
339261c4a9
Load the dictionary and sanity check it against the index.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@430 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 18:04:13 +00:00
26e84d7fd6
Added index iteration for ReferenceSequenceFile interface compatibility.
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Added better error checking for querying past the end of a contig.
Lots more testing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@429 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 17:17:11 +00:00
3fda8613c3
* minor formatting changes
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* support for "extended" output
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@428 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 15:11:05 +00:00
12407b5b1a
Deleted the old file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@427 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 13:55:01 +00:00
6db9127f90
Added changes to shattering, refactored SAMBAM into SAM
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@426 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 13:52:56 +00:00
182626576f
Basic indexed fasta POC in place. Requires a more complete implementation of the ReferenceSequenceFile interface,
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and much more testing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@425 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 13:46:56 +00:00
7949e377e4
Intermediate commit. Refactored some simple base manipulation stuff into BaseUtils.java. Generalized some likelihood computation logic to make future possible EM-ing easier.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@424 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 04:18:07 +00:00
d0b8d311e6
Can now optionally print the read and the alignment region of the reference.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@423 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 04:10:30 +00:00
d4aaa1bef4
* fixed (with Matt's help) the argument parsing
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* outputting UCSC wiggle format
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@422 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-15 02:17:39 +00:00
24722a442e
Slight code cleanup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@421 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 22:21:36 +00:00
e6fb122d7d
Added some fixes and new iterator tests
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--This lin e, and those below, will be ignored--
A gatk/iterators
AM gatk/iterators/BoundedReadIteratorTest.java
M gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@420 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 22:19:36 +00:00
13b0995d54
Adding an iterator that bounds the number of reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@419 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 22:18:31 +00:00
72a3d84ed2
General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@418 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 22:13:10 +00:00
baae98c6d5
and don't allocate new 200M string every time please, just pass byte array!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@417 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 21:55:33 +00:00
9d56355abe
bug fixed when reference name was passed as a string instead of actual reference bases
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@416 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 21:46:27 +00:00
222c4e5865
Commented out some debugging lines
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@415 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 20:15:41 +00:00
49d76014d1
Commented out a debugging line
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@414 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 20:15:11 +00:00
b39e584787
Primary or secondary bases that got a quality score of literally zero led to unfortunate infinities. Added an epsilon (1e-5) to every prob.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@413 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 20:04:49 +00:00
d28e9f9b98
search over q's for finding argmax[q] p(D|q)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@412 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 19:15:45 +00:00
96248cdec4
Added some output to all the classes, including build in runtime analysis
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@411 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 19:14:53 +00:00
647827b18c
Transitioned indel code to use GATK and Walkers
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@410 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 19:14:15 +00:00
b363eedd2c
Deal with screwy reads by changing logic to determine whether we are
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past the last interval
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@409 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 19:13:16 +00:00
0629f79049
Moved fasta support files into their own package.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@408 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 18:13:23 +00:00
7a4a5a17c0
Made sequence index compatible with Aaron's junit changes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@407 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 17:53:20 +00:00
88ebf1a05b
Fied some documentation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@406 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 17:41:38 +00:00
186c799ffc
Class to read an .fai file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@405 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 17:37:18 +00:00
704f1bd634
It helps if I check the new base class in with my changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@404 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 17:18:16 +00:00
4b3578e1de
Added the base test case, fixed the rest of the test cases to follow suit. Added more verbose output to ant for junit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@403 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 17:11:38 +00:00
961dbbd4ef
Now output bases and qhat and qstar into the GFF.
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Quals coming soon (four-base)
QHAT : Most likely alt allele freq (unconstrained by number of chromosomes).
QSTAR : Most likely alt allele freq (constrained by number of chromosomes).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@402 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 15:23:00 +00:00
dafdff1974
All bases are now indexed as A:0, C:1, G:2, T:3.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@401 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 14:49:43 +00:00
40ea22eb17
Added some methods to return the cross-talk partner base of a given base or base index.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@400 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 14:49:12 +00:00
eb4b4a053b
A bunch of updates to the SAM/BAM data source, along with test cases for the merging of multiple files (it works!).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@399 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 14:19:20 +00:00
30121534ed
Outputs the secondary bases and quals (if available) in verbose mode. Prefixed with the tag 'SQ='.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@398 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 13:58:28 +00:00
998fad76c6
Some utility methods for creating pileups of secondary bases and secondary quals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@397 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 13:57:54 +00:00
8b2c2e677b
Uses the cleaner new GenomeLoc(read) syntax
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@396 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:55:43 +00:00
1cee7948ab
Added lots of assertions to check for problems.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@395 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:55:19 +00:00
794360c410
Added verbose option to show mapping qualities and base qualities as ints!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@394 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:54:48 +00:00
cc75e8f712
Uses the cleaner new GenomeLoc(read) syntax
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@393 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:53:58 +00:00
11377ef390
Added lots of assertions to check for problems. The current GenomeLoc needs to be cleaned up and refactored but at least it runs. We need unit tests ASAP
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@392 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:53:08 +00:00
bb666ce392
Added mappingQualPileup function for use in the verbose mode of Pileup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@391 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:51:26 +00:00
bc43c0eefc
there are really cases when we can not merge until we get just two pilesant now we do not crash in those cases but print a warning and just show the resulting n piles even when n>2
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@390 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 00:45:47 +00:00
andrewk
ebanks
aaron
kiran
hanna
depristo
jmaguire
kcibul
asivache