a8a2d0eab9
added support for the -M option in traversals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@935 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-08 15:12:24 +00:00
e2ed56dc96
Add a MAX_READ_GROUPS sanity parameter.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@934 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-08 13:57:43 +00:00
9f35a5aa32
Insidious bug: clipped sequences (S cigar elements) where a) processed incorrectly; b) sometimes caused IntervalCleaner to crash, if such sequence occured at the boundary of the interval. The following inconsistency occurs: LocusWindow traversal instantiates interval reference stretch up to rightmost read.getAlignmentEnd(), but this does not include clipped bases; then IntervalCleaner takes all read bases (as a string) and does not check if some of them were clipped. Inside the interval this would cause counting mismatches on clipped bases, at the boundary of the interval the clipped bases would stick outside the passed reference stretch and index-out-of-bound exception would be thrown. THIS IS A PARTIAL, TEMPORARY FIX of the problem: mismatchQualitySum() is fixed, in that it does not count mismatches on clipped bases anymore; however, we do not attempt yet to realign only meaningful, unclipped part of the read; instead all reads that have clipped bases are assigned to the original reference and we do not attempt to realign them at all (we'd need to be careful to preserve the cigar if we wanted to do this)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@933 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-08 05:20:29 +00:00
3a8219a469
use knowledge from other reads to find a consensus
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@932 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-07 21:22:17 +00:00
596773e6c6
Cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@931 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-07 20:25:08 +00:00
98396732ba
Bug fixes for Andrey
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@930 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-07 18:19:51 +00:00
b48508a226
indelRealignment() signature changed. The only difference about consensus sequences is that they are passed along with alignment cigars that start inside the sequence, while for 'conventional' reads cigar always starts at position 0 on the read. Logically, indelRealignment() should not know what 'consensus' is. Instead, now it receives an additional int parameter, start of the cigar on the 'read' sequence
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@929 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-07 17:42:19 +00:00
9eb38c0222
mostly synchronizing with the main branch. Based on anecdotal evidence (too few examples in the data), realignment (shifting indel left across a repeat) works correctly on non-homonucleotide repeats
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@928 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-07 16:39:16 +00:00
c6634e3121
cleaned up some code and minor bug fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@927 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-07 03:14:21 +00:00
99c105790b
Now indelRealignment should be correct... The old version could only condense to the left homo-nucleotide indels. New version should be able to detect and shift left arbitrary repeated sequence (e.g. deletion of ATA after ATAATAATA will be shifted left to the first occurence of ATA on the ref! NOT THOROUGHLY TESTED YET, will test tonight../somaticIndels.pl --dir . --cutoff 100 -filter EXON --mode SOMATIC --condense 5 --format bed > 0883.indel.somatic.exon.100.bed
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@926 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-06 23:54:07 +00:00
3b4dc6e7b5
added sequencePeriod(String seq, int minPeriod) - finds smallest period equal to or greater than minPeriod for the specified text string seq; this is a trivial (hopefully correct) back-of-the-envelope implementation for a well-known and well-studied problem; there should be more efficient algorithms in the wild
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@925 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-06 23:05:24 +00:00
40ac3b7816
Inject read group into covars_out file's toString output. Continue fixing systematic bug in the code where flattenData is not joined to the read group.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@924 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-06 20:43:28 +00:00
0bb4565798
added AlignmentUtils.getNumAlignmentBlocks(read) - a faster alternative to read.getAlignmentBlocks().size(); IntervalCleaner updated accordingly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@923 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-06 19:35:21 +00:00
92b054b71b
moved another variant of numMismatches to AlignmentUtils
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@922 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-06 18:07:48 +00:00
7018dd1469
moved another variant of numMismatches to AlignmentUtils
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@921 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-06 18:05:29 +00:00
ac5b7dd453
Fixed order-of-operations bug.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@919 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-06 03:22:56 +00:00
819862e04e
major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@918 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 23:34:37 +00:00
400399f1b8
fixed (?) a bug in insertion realignment
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@917 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 22:04:37 +00:00
34bb43a6c8
Saw that one of the offsets needed to be changed from - 1 to -2 and changed the wrong damn offset. Fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@915 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 19:18:34 +00:00
4623a34ad3
Fix bug in realigning insertion cigar strings
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@914 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 18:46:41 +00:00
199be46c36
changed the warning that is outputted when the GenomeLoc constructor can't find the given contig in the reference.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@913 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 15:49:03 +00:00
092a754071
Make sure indel position from SW alignment is leftmost possible
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(and improve printouts)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@912 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 15:36:10 +00:00
37efd78c7e
fixed the logger call so we get output that indicates this class generated the message
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@911 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 15:02:17 +00:00
b323c58ef2
add a place to store the walker return value, along with a method to retrieve it
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@910 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 14:41:42 +00:00
36fb6ca3c5
Allow user to specify the compression to be used when writing out BAM files.
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Updated most of the walkers to reflect this change.
Now it won't take forever to write BAMs!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@909 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 08:48:34 +00:00
c1792de44f
First pass at fixing the incorrect border-case behavior of the cleaner
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@908 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 07:55:06 +00:00
9da04fd9ac
Cleaned up error warning in case no PL groups are present.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@907 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 03:14:17 +00:00
45eeefbb80
Deal with randomly occurring unmapped reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@906 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 02:55:53 +00:00
fdfc3abf80
Better handling for case where PL attribute is missing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@905 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-05 02:52:30 +00:00
9689bb3331
Very early draft of script integrating the covariant counting / logistic regression. Deleted some unused code and spurious debug info.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@902 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 22:52:11 +00:00
109bef6c08
We're no longer in the read-dropping business.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@901 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 22:37:51 +00:00
4d880477d6
Deal with ends of contigs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@900 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 20:09:53 +00:00
40bc4ae39a
The building blocks for segmenting covariate counting data by read group.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@899 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 19:55:24 +00:00
13be846c2a
qualsAsInt argument for Pileup -- fixing stupid bug [again]
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@898 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 18:52:12 +00:00
97c8ff75dd
qualsAsInt argument for Pileup -- fixing stupid bug
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@897 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 18:51:17 +00:00
9de3e58aa8
qualsAsInt argument for Pileup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@896 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 18:37:39 +00:00
4d654f30d4
slightly improved error message printed upon failure to parse interval list file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@895 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 18:24:43 +00:00
bcc7bacba1
added List<Transcript> getTranscripts(); also more comments added
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@894 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 16:25:14 +00:00
b492192838
Pairwise SNP distance metrics now enabled
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@892 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-04 00:11:29 +00:00
8672ae6019
Now seeing results from the training data. There are still some critical problems in the quality of the output, but we're at least getting training output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@891 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-03 20:41:07 +00:00
4e41646c88
print out stats for Andrey
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@890 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-03 17:45:35 +00:00
dfe464cd81
Updated CovariateCounterWalker to be read group aware
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@889 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-03 10:06:06 +00:00
40af4f085c
Adding some utilities to test unmapped reads
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@887 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-03 07:40:34 +00:00
fa93661133
Eric wins the prize for pointing out that doubles weren't valid command-line arguments. Made all primitive types parseable as command-line arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@884 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 22:41:10 +00:00
107b5d73b5
The flagStatReadWalker generates the exact same statistical output as the samtools flagstat command, so the two outputs can be diff'ed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@883 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 21:23:56 +00:00
a1218ef508
changed default value for failure output
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@880 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 19:32:29 +00:00
7e7c83ddca
fixing insidious bugs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@879 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 18:33:45 +00:00
6e60cddfed
A fix for the 'rod blows up when it hits a GenomeLoc outside the reference' issu
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e. Really a stopgap; error handling in the RODs needs to be addressed in a more comprehensive way. Right now, hasNext() isn't guaranteed to be correct.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@878 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 18:14:46 +00:00
ad5b057140
parameterized a bit more
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@877 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 17:58:26 +00:00
587d07da00
Merged functionality of two python scripts into LogRegression.py, some clarity updates to covariate and regression java files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@876 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 16:55:05 +00:00
82aa0533b8
added some more documentation to the GLF writer and it's supporting classes, and some other fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@875 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 14:53:58 +00:00
c4cb867d74
basic clustering of reads to reduce artifacts
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@873 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 02:54:21 +00:00
e712d69382
GLF writing support
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@872 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 21:30:18 +00:00
417f5b145e
Strand test and misc touch-ups
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@871 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 17:13:21 +00:00
fc91e3e30e
equals signs can be important
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@870 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 16:56:21 +00:00
4edb33788b
added a fix for a bug Andrew found
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@869 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 16:53:56 +00:00
b7defeae83
Fix bug in unit tests created by new filter in TraversalEngine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@868 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 15:50:44 +00:00
fc7320133c
Cleaned up error when fasta index is missing. Code still throws an exception, but the message is more direct (no more 'error while micromanaging') and tells the user to run 'samtools faidx' to fix the issue.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@867 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 15:34:38 +00:00
f19d7abba9
Added geli compatibility mode to SingleSampleGenotyper, to enable easy linking to the geli2popsnps.py script
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@866 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-01 14:32:12 +00:00
4d6398cef9
a lot of people have been asking me for the equivalent of the old "PrintCoverage" command from Arachne. Even though I show them the pileup, and they agree that's more accurate/complete, they don't want to modify their scripts and/or write a translator. It was simple enough to write, so here it is.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@863 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-31 01:45:23 +00:00
c04b67c969
Basic instrumentation support for the hierarchical microscheduler.x
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@862 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 22:19:27 +00:00
c8347c3c94
set proper package name (...walkers.indels), remove couple of unused import statements
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@861 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 22:02:14 +00:00
c549c34caa
still in development and testing; kinda works
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@860 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 21:59:03 +00:00
c252fec1bc
synchronizing, no real changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@859 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 21:56:14 +00:00
eafdba7300
more efficient implementation of line parsing, runs at least 1.5 times faster
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@858 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 21:09:06 +00:00
8761ab3aff
Oops. IteratorPool was occasionally creating too many RODIterators in cases where some reference-ordered data was missing. Fixed by better tracking position of RODIterator.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@857 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 21:00:31 +00:00
d601548d53
added reallocate(int[] orig_array, int new_size) and int[] indexOfAll(String s, int ch); the former is self-explanatory, while the latter returns array of indices of all occurences of ch in the specified string
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@856 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 20:15:00 +00:00
a1edb898ef
Make criteria for determining whether to stop and merge inputs more sane.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@855 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 18:08:18 +00:00
fe3b843b65
intercept NullPointerException and rethrow it with (marginally) comprehensible error message when an attempt to get class source code location fails
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@854 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 15:56:55 +00:00
e0803eabd9
enabled underlying filtering of zero mapping quality reads, vastly improves system performance
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@853 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-29 14:51:08 +00:00
1f93545c70
Always opt to merge dictionaries when creating a SAMFileHeaderMerger.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@852 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 22:38:16 +00:00
0cf90b6f8a
Tie into sequence merging code in the latest version of picard.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@851 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 21:48:35 +00:00
b43deda6c9
iterative changes to GLF files; also a test of checking-in over sshfs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@850 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 20:24:30 +00:00
5e8c08ee63
Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@849 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 20:13:01 +00:00
19f9ac2b05
Realign existing indels (from the aligner) to leftmost position
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@848 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 04:56:51 +00:00
aa17c4a468
Farewell, functionalj. You promised much, but you could not deliver.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@847 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 01:35:49 +00:00
d275c18e58
adding some objects we need for the GLF format.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@846 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 22:32:25 +00:00
ce6a0f522b
First incarnation of the population-based SNP analysis tool. Also bug fixes throughout the GATK
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@845 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 22:02:24 +00:00
a11bf0f43e
Basic unit tests for ReferenceOrderedView, ShardDataProvider. Addressing GSA-25.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@844 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 21:15:01 +00:00
e533c64b8f
Walker to pull out the reference for given intervals and emit them in fasta format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@843 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:39:09 +00:00
5c6163ecbf
Removing the old reads traversal.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@842 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:36:11 +00:00
c7b032cc88
missed a file in the add.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@841 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:27:38 +00:00
3c3cd5bb64
Moving some of the data sharding around. A new shard catagory now exits, INTERVAL. This saved a lot of code that was mirroring the same approach in both the read and locus shard strategies.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@840 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:24:31 +00:00
99524ab6d0
package name corrected
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@839 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:20:43 +00:00
b76f8c4eb5
moved from playground to gatk
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@838 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:18:33 +00:00
c3678c7bb9
moved from playground to gatk
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@837 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:18:08 +00:00
5b310e48f5
changed to use factored out Transcript class; some docs added (not much)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@836 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 18:17:23 +00:00
ae0bac5696
'made public' implies the 'public' keyword, actually...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@835 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 17:57:01 +00:00
41c1a62ac4
formerly private class, factored out and made public. Represents a transcript annotation (transcript id, genomic location, genomic intervals for all exons present in this transcript, etc)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@834 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 17:52:38 +00:00
8edba13ded
Unit tests for the reference views. Partially addresses GSA-25.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@833 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 17:49:45 +00:00
9bd6489f8e
Output indels in the format appropriate for low-coverage indel submission
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@832 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 17:32:15 +00:00
919e995b7f
-Moved my walkers to indels directory
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-Removed entropy walker and replaced it with mismatch (column) walker
-Some improvements to the cleaner (more to come)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@830 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 16:34:24 +00:00
864a1e81e3
Delete stale class from previous rethink of the traversal engine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@828 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 13:52:03 +00:00
6fab1a64fa
Started work on GLF input / output basics. Do not use.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@827 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 22:49:59 +00:00
b81135c606
bug fixed; this rod seems to work now...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@826 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 22:25:34 +00:00
a488d2dbb2
Lazy creation of output streams. Only create output streams when absolutely necessary.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@824 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:56:57 +00:00
ab7bb5800a
forgot to remove debug print statement
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@823 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:38:27 +00:00
568a0d3c27
exon coordinates are now parsed correctly (?). IF DELIMITER IS THE LAST CHARACTER IN A STRING, String.split() DOES NOT return empty field as the last one; instead, the last field returned will be the one immediately before such delimiter! Wicked.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@822 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:36:50 +00:00
f4119c17de
still working on it...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@821 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:07:38 +00:00
d73f2e95cc
refseq added to the list of known rod types
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@820 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:06:44 +00:00
23b7a28015
simple walker that works off pre-computed tumor/normal genotyping calls (e.g. samtools pileup). Collects overal stats and also writes somatic variants into IGV-compatible bed file if asked to. NOT finished. NOT tested
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@819 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:05:47 +00:00
8f1cabd33d
cmd line args changed - again; internally uses VariantType enum
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@818 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:03:58 +00:00
9ef1a21112
minor changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@817 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 21:03:06 +00:00
d994544c47
Added back end code support for Sharding based on genomic location for reads. Changed the sharding
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code to take GenomeLocSortedSet instead of a list<GenomeLoc>, and added a bunch of much simplier
and cleaner test cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@816 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 20:57:46 +00:00
4edcdffe45
refseq annotation track: should be able to provide (multiple) transcript annotations available over a given genomic position. NOT finished and NOT tested!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@815 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 20:07:15 +00:00
149cc9989b
spaces!!!!!!!!!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@814 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 19:40:25 +00:00
c2df35b7fe
- get leftmost position of indel correct
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- don't try to clean reads with mapping quality of 0
- un-deprecate
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@813 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 17:24:58 +00:00
54bb643d19
Validated Mark's assertion that GSA-27 is fixed. Also did some cleanup on the pileup walker so that it doesn't output to System.out.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@812 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-26 15:58:21 +00:00
008d677bea
Fixed ValidatingPileup to work with Andrey's new rodSAMPileup -> GenotypeList type hierarchy.
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Fixed reference-ordered data validation system to validate class hierarchies instead of specific class types.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@811 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-23 20:50:28 +00:00
d056f9f3e8
Changed the name to reflect the sorted nature of the set, added some fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@810 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 22:34:24 +00:00
831d430025
Added a collection for storing GenomeLocs, that also has functions for removing by genomic region (that may span multiple GenomeLoc's in the collection), and adding regions, which are then merged with any overlapping regions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@809 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 21:52:40 +00:00
34413362fd
Bugfix: handle case where queue is empty.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@808 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 21:45:22 +00:00
ec2e8d5726
Fixes for getting ValidatingPileup running in parallel.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@807 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 21:20:24 +00:00
cd80e3f372
Replaced dumb training function with a version that creates a training set slightly more sensibly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@806 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 19:34:33 +00:00
02c0afdb85
Added the ability to specify the sorted, unaligned bam and/or the sorted, aligned bam such that broken computations can be restarted.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@805 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 19:33:34 +00:00
454a6d1df7
Fixed an egregious error in simpleReverseComplement wherein the RC'd string would be composed entirely of the last base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@804 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 19:32:20 +00:00
2a5be1debe
Cleanup in datasources.providers namespace. Make it easier for others writing traversal engines to use.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@803 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 19:12:00 +00:00
02fc4f145f
refactoring: a couple of general purpose (hopefully useful?) methods/classes extracted into a standalone utils class
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@802 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 18:54:40 +00:00
4b718688d5
no changes, really, just synchronizing (instead of reversing) to increase the amount of entropy
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@801 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:27:28 +00:00
893f1b6427
updated
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@800 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:25:50 +00:00
a9dfbfb309
internal changes and some refactoring. slightly different final report. Now can take tracks that implement either Genotype or GenotypeList; takes an arg specifying what variants to look for (POINT - aka snp - or INDEL); takes an arg specifying whether default ref/ref call of one type (INDEL/POINT) should be implicitly assumed if another call (POINT/INDEL respectively) was made at the same position [this is probably most useful for indels and only (?) for sam pileups: if we have only point mutation call at a given position, it does mean that we do have coverage, and that there was no evidence whatsoever for an indel, so we have an implicit 'no-indel' call]
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@799 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:25:09 +00:00
d5bb4d9ba9
Auxiliary class that can read one line from samtools pileup file. Used by rodSAMPileup to read pairs of lines as needed. NOTE: this class implements Genotype and (a trivial) GenotypeList, but it is NOT a rod!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@798 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:20:01 +00:00
732fed9aad
ALERT, ALERT! rodSAMPileup is now a GenotypeList, not a Genotype! Now it can intelligently read full samtools pileup files (containing, in general, both point and indel genotypes at the same position). No need to split/synchronize pileups from different individuals anymore, hooray!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@797 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:17:59 +00:00
26633957d9
Genotype interface is extended: now it requires implementing object to be able to tell whether it isPointGenotype() or isIndelGenotype() (and the contract requires, e.g. alleles to be represented differently)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@796 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:14:46 +00:00
d9fc84f1e3
actually checking in the first pass
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@795 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:13:27 +00:00
8773b3a430
a trivial wrapper interface for the objects capable of holding 'full' genotype, i.e. both point (as in ref/snp) and indel variants at the same reference position
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@794 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:12:01 +00:00
7a979859a9
Intermediate checking for evaluation -- now supports transition / transversion evaluation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@793 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 17:05:06 +00:00
f2ea193149
For some reason the apostraphes in the comments were throwing annoying
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compile-time warnings: "unmappable character for encoding UTF8"
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@792 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 14:07:07 +00:00
9902ce8073
properly flush the gzip output stream. this was a subtle inheritance bug.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@791 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 13:57:58 +00:00
63caca31bf
minor update in report printout format
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@790 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-22 13:56:09 +00:00
7afc10fd6f
updated, reports more stuff now, including stats for external consistency checks
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@789 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 22:28:18 +00:00
30c63daf89
More improvements to the duplicate quality combiner, making progress towards a clean system
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@788 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 22:26:57 +00:00
65995887fc
Releasable version of the Pileup walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@786 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 22:25:37 +00:00
dc17a5661d
Better accessors for dealing with second base prob pileups
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@785 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 22:25:16 +00:00
d261459c48
Useful function to create a string with N copies of a same char
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@784 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 22:23:52 +00:00
287bb52e81
Refreshes the mount points that we'll be using (so that the program will play nicely with LSF).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@783 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 20:36:12 +00:00
b5ad5176f7
stick headers on the output tables
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@782 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 20:35:50 +00:00
83e1454a11
Added a method to determine the fraction of a sequence that's taken up by the most frequent base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@781 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 20:35:31 +00:00
bdf772f017
Added test for determining the fraction of a sequence that's taken up by the most frequent base (quick-and-dirty homopolymer testing).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@780 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 20:35:08 +00:00
d61a5261c1
Better integration of reference-ordered data into the data sharding system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@779 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 20:09:32 +00:00
0d58e4ccc9
-check original alignments for indels when computing mismatch score
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-move logging to debug
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@778 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:55:42 +00:00
5f67914b08
Added loads of documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@777 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:40:47 +00:00
1a9d5cea29
Added a method to reverse-complement a String object, preserving 'N' and '.' bases.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@776 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:39:39 +00:00
a687c6bc03
Added a method to refresh an NFS mount point (necessary to prevent NFS flakiness when running on the LSF farm.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@774 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:31:54 +00:00
324ef9cbd1
Test class for PathUtils.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@773 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:31:22 +00:00
8515247575
Adding some functions I keep reinventing, especially for testing purposes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@772 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:30:44 +00:00
e6200fe5b5
don't ignore reads when maxReadLength isn't set
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also, print out LOD score for cleaning
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@771 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:24:10 +00:00
0219d33e10
QualityUtils: added reverse function to reverse an array of bytes (and not complement it), BaseUtils: split qualToProb into itself and qualToErrProb, CovariateCounterWalker and LogisticRecalibrationWalker: several changes including a properly acocunting (only partly complete) for reversing AND complementing bases that are negative strand, PrintReadsWalker: created option to output reads to a BAM file rather than just to the sceern (useful for creating a downsampled BAM file)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@770 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 18:30:45 +00:00
7e77c62b49
auxiliary class, a simple struct to keep together info like numbers of covered, assessed, ref/variant bases across the sample
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@769 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 16:30:16 +00:00
7e5e422591
ReferenceOrdereData now inspects the ROD class using reflection. If the ROD declares a static Iterator<ROD> createIterator(String rodName, File rodFile) factory method, it is wrapped and used by the ReferenceOrderedData to read records from rodFile. If the ROD does not provide such factory method, the old behavior is the default: ReferenceOrderedData uses its own simple default iterator to read the file line by line (assuming there is only one line per record/position).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@768 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 15:23:22 +00:00
26dd3cd50e
Cleanup. Move filtering functions closer to where they're used.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@767 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 21:42:48 +00:00
e7a6f8cdc4
Removed evidence of a previous incarnation of data sharding.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@766 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 20:48:33 +00:00
3cad580655
Catch and rethrow the walker's required argument, so that command-line arguments will be displayed when the GATK throws an argument exception.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@765 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 19:17:16 +00:00
dc748d9c9c
Integrate more feedback on command-line argument system. Focus on help
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formatter: separate required from optional but otherwise keep ordering
the same, reorder GATK arguments by usage.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@764 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 19:01:25 +00:00
34f9820299
update mapping quality score and edit distance attribute for reads when they are cleaned
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@763 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 17:51:31 +00:00
57918de753
add the @Requires for this walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@762 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 17:03:12 +00:00
747521c849
Fixed the simplest of typos.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@761 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 16:00:30 +00:00
e48078b476
Updated to reflect change to BasecallingReadModel constructor.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@760 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 15:43:26 +00:00
505f588768
Forgot to say that the mate is unmapped too. This is necessary to prevent SAM-JDK from yelling at me about an invalid SAM file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@759 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 15:38:51 +00:00
96e73e496a
Delete deprecated old-school traversals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@758 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 14:57:17 +00:00
b840dd1320
Added some code to change the instrumentation for tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@756 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 05:15:27 +00:00
6c5fbb988b
Now basecalls an entire read (both ends of the pair, barcode... everything) at once. After, RawRead and FourProbRead can be asked to return a specified subset (corresponding to the ranges specified for each end of the read.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@754 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 00:09:20 +00:00
e293d65ede
Refactored to allow the user to specify the range of cycles they wish to call. Simply specify a single range (i.e. '0-75') or two ranges ('0-75,76-151'). This allows single and paired-end read processing to coexist happily. Also implements annotation of an aligned bam file (which should hopefully fit in under two gigs now, but I'm waiting on a bug fix or a clarification from the Picard team.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@753 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 00:07:24 +00:00
08c9f4d86b
Renamed to BasecallingTrainer.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@752 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 00:03:46 +00:00
01a3cb27c7
@Required / @Allows flags for main arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@751 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-19 23:26:17 +00:00
40dbc21df7
Moved ParseException to it's own file and made it public.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@750 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-19 14:42:44 +00:00
ff798fe483
Reintroduce support for interval-based traversals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@749 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 22:54:18 +00:00
3441795d9c
better handling of edge cases (zero coverage, reference mistakes, etc.)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@747 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 18:04:37 +00:00
7c615c8fb0
Some changes to the system for annotating a pre-aligned bam file. Doesn't fit within 2gigs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@746 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 17:42:08 +00:00
a39c8839c8
print percentage sign!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@745 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 14:38:20 +00:00
c10741e9f5
Rename TraverseLociByReference to TraverseLoci to represent its new function.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@743 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 01:31:57 +00:00
e6ce80c8e3
Fix for GSA-44...don't throw exception when user specifies -h.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@742 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 00:42:00 +00:00
d35e20ce21
Better error checking for missing .dict file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@741 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 21:57:12 +00:00
7161b8f927
Disable support for short name values directly abutting their arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@740 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 16:09:32 +00:00
d152c2b911
New GATKArgumentCollection caused a subtle bug with argument grouping and the help system. Fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@738 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 14:54:25 +00:00
94e324b844
Write N for the alt allele when we're hom-ref.
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Stop EM loop when we've converged (likelihood[t-1] == likelihood[t]).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@737 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 13:58:11 +00:00
bd53bc18f9
added new required annotations
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@736 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 12:24:06 +00:00
28bf7ec8ad
Aesthetic cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@735 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 04:09:23 +00:00
a0464633fd
Whoops. Changed denominator from reads to bases.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@734 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 03:42:25 +00:00
5d60efc498
Factored out some simple stats accumulation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@733 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 03:37:57 +00:00
81fac73c01
LOD checks for normal and brute force versions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@732 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 02:56:03 +00:00
527df6e57b
Massive speed-up, clean-up and tabular output.
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This program is going to rule.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@731 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-16 16:52:40 +00:00
3b57a35009
don't be tricked by multiple read groups with the same sample id!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@730 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-16 15:28:55 +00:00
947bac5cdc
vast speedup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@729 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-16 15:27:58 +00:00
6f1559bd77
Cleaned up a bit. Added some documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@728 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 21:22:24 +00:00
2c4de7b5c5
Switch TraverseByLoci over to new sharding system, and cleanup some code in passing read files along
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the pathway from command line to traversal engine.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@727 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 21:02:12 +00:00
f33f3c0434
added LOD threshold for determining when to clean
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@725 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 20:23:59 +00:00
99d4ebc26d
Added functionality to return the final accumulator of a traversal, so external tools can get the result of a walker.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@724 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 20:20:27 +00:00
dae77bf14a
Fixed a typo in a comment.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@723 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 20:07:31 +00:00
bfc40f54f0
Nicer output when training off of perfect reads. Not that that works yet...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@722 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 20:07:08 +00:00
d1f3000afa
bed-style output for IGV
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@721 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 17:58:44 +00:00
36db44620b
Improved output. Can optionally limit the number reads actually called.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@720 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 00:07:57 +00:00
7834b969b4
Better interface to the tabular ROD, now makes writing files easier. Also has corresponding test files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@719 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 23:20:11 +00:00
50f32b7f61
Added a shard strategy for the reduce-by-interval traversals. Also fixed bugs that I found along the way.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@718 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 21:20:18 +00:00
0f8e6061b6
Simple interface improvements
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@717 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 21:08:09 +00:00
8e9e2f4502
Revised ROD system. Split the system in Basic type and interface. Enabled more control over rod accessing, including an initialize() function to fetch headers and other options from the file. Added general tabular rod, which has a named columns and supports a map<String,String> interface. Comes with shiny new Junit system for RODs. Also, added simple python script for accessing picard data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@716 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 21:06:28 +00:00
67293168e7
Support periods in sequence names.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@715 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 20:17:57 +00:00
641afc4e76
fix a crash in the event that the input file has no read groups!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@714 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 19:27:41 +00:00
d8c1b010f1
Fixing the naming of the function I checked in earlier.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@713 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 19:27:10 +00:00
5858f20902
Documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@712 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 18:58:43 +00:00
68c9455c0f
Moved the base complement method to BaseUtils.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@711 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 18:57:48 +00:00
3761c0900b
Added Bustard vs. Four-prob percent bases consistent output.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@710 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 18:01:41 +00:00
7a1f85ff86
option to print out the indels found by the cleaner to a file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@709 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 17:50:08 +00:00
b62bddee42
The header was never being set.
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Added this hack for now and will alert the authorities ASAP...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@708 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 17:18:51 +00:00
959cf09d4b
Removed some debugging print statements.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@707 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 17:12:42 +00:00
2f42a643a8
A new, much simpler (and now, complete) driver program for four-base probs. Serves as a model for anyone who wants to write their own driver program that trains and calls with data from a different source than the raw Illumina data.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@706 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:58:22 +00:00
5824dea0c1
Trains and calls a read at a time rather than a base at a time (which, given it's name, it should have done in the first place)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@705 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:57:00 +00:00
e4770885fd
The four-probs for all bases in a single read. Some utility functions for generating the primary and secondary base strings, as well as generating the SQ tag byte array in a manner that's consistent with the Bustard base calls (meaning the primary Bustard call and the secondary Four-Prob call are not permitted to be the same).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@704 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:55:49 +00:00
fdd123fe16
A parser the raw Illumina data. Allows one to arbitrarily jump from one tile to another.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@703 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:53:07 +00:00
7aa90757ac
Moved the iterators over to the StingSAMIterator interface. This will help us ensure that iterators that need to be closed get closed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@702 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:52:18 +00:00
6d98234555
Holds raw intensities, sequence, and quality scores.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@701 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:52:03 +00:00
241de0b235
A class that implements multiple training strategies and presents the training data in a common form.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@700 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:51:29 +00:00
64c65c7751
New methods to generated compressed SQ quality elements in line with the SAM spec.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@699 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:50:31 +00:00
c3b2c66911
The GATK doesn't need the rest
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@698 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 16:20:45 +00:00
0215905bb6
Added an adapter class, that will adapt plain iterators and closeable iterators of SAMRecords into STingSAMIterators. Also unit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@697 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 15:17:32 +00:00
5dda448ae0
1. Add printouts for the cleaner
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2. First pass at the entropy interval walker (still needs work)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@696 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 13:59:48 +00:00
80c13f7127
Added a getter for command-line arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@695 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 13:55:52 +00:00
307c6e4ecf
Oops. Forgot to add new file to svn.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@694 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-14 00:52:30 +00:00
d14cab0be7
Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@693 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 21:32:05 +00:00
7b59f63f12
and don't forget to close sam writer after we are done...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@692 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 20:46:36 +00:00
de0cce87ea
new optional arg added that allows to specify a separate bam file to send all piles that fail to realign to; plus minor fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@691 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 20:24:23 +00:00
12ae3a22b6
Break locus context data access providers into modular components in preparation for traverse by loci.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@689 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 18:51:16 +00:00
7084ecdeb6
a few changes; checked in to allow debugging.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@688 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 15:50:48 +00:00
5b47c5ab6c
fixing kiran's busted build
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@686 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 21:29:04 +00:00
4f2c8bf0a3
Fixed an import statement that broke when all the files were moved to this directory.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@685 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:43:16 +00:00
cedc4c9ccb
Refactored into oblivion.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@684 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:33:07 +00:00
4e4767e5de
Moved to org.broadinstitute.sting.secondarybase
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@682 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:26:43 +00:00
219eb60716
Added newly-required documentation to arguments so that build can complete successfully.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@681 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:26:10 +00:00
688358190c
Moved secondary base stuff out of playground for the purpose of making it a core utility. Modified package names and imports such that things would build properly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@680 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:24:18 +00:00
8079acb1d3
basic step0 implementation
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@679 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:49:39 +00:00
57ecb7fbf1
Nicer reporting functions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@678 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:48:30 +00:00
ee99320c83
Removed at Mark's request.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@677 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:48:21 +00:00
f1de3d6366
Minor tweaks to how probs are supplied.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@676 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:47:41 +00:00
095dacd154
Experimental refactoring.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@675 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:46:50 +00:00
758f8aa89b
Experimental refactoring.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@674 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:46:34 +00:00
1518f8f9bf
Update training data creation in CovariateCounterWalker to output much smaller files by counting the number of occurences of each data point combination rather than outputting a line for each data point (i.e. each base). Also fixed bug in LogisticRecalibrationWalker where a null SAMHeader was being pulled from a function that is now marked deprecated.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@673 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:23:14 +00:00
4c12df372c
Dumb, dumb bug.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@672 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 19:21:33 +00:00
6e69193e3c
Deprecated calls to getSamReader on both the GenomeAnalysisEngine and the TraversalEngine. This call fails in the new style traversals, but it won't disapear until the cut-over to the new traversals is complete.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@671 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 18:52:42 +00:00
630066cc0a
1. Merge LocusWindows whose reads overlap.
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2. Fix bug (we weren't clearing the "to emit" list)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@670 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 17:33:23 +00:00
9f942fdfa0
Added code to correct the violation of the parsing interface. Now the analysis type resides in the command line arg, but is stored into the argument collection before it's passed to the genomeAnalysisEngine.
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Also fixed a bug where we'd exception-out if we didn't provide a interval region.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@669 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:33:55 +00:00
c4d89997ca
put in a dummy sample_name so it'll compile
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@668 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:12:42 +00:00
c8d7223789
do pooled calling properly for 1kg
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@667 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:12:13 +00:00
313a6d0fb5
lots of changes to facilitate calling indels and 1kG
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@666 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:11:42 +00:00
add7b6cf65
add sample_name to constructor, misc bug fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@665 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:10:17 +00:00
0267ccae7f
add code for computing indel genotype likelihoods
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make reference lods negative
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@664 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:09:29 +00:00
11723fbcc2
added method indelPileup. Generates a pileup of indel alleles given reads and ofsets (as from a locus walker).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@663 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 15:08:24 +00:00
ee9077fc69
LocusIterator iterated through LocusContexts, which was fine until now when we need something
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that iterates through loci (GenomeLocs). Rename LocusIterator to LocusContextIterator.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@662 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 13:54:57 +00:00
608948210c
Check for a reference before extraction.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@661 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 13:29:44 +00:00
32696b13f5
Fixed method override issue with old-style traversals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@660 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 01:22:18 +00:00
862b8a6787
intervals_file + genome_loc => intervals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@659 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 01:04:18 +00:00
0bca588629
Botched some boolean logic.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@658 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 22:53:52 +00:00
23e9e29964
Changed reads traversals from providing a LocusContext from which the reference sequence
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could be extracted to a char[] containing the reference bases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@657 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 22:45:11 +00:00
052819bed5
Switched dependencies of GenomeAnalysisTK to depend on GenomeAnalysisEngine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@656 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 22:33:00 +00:00
ff1b92acc4
Switch over to the GenomeAnalysisEngine/CommandLineGATK system from the GenomeAnalysisTK code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@655 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 22:05:58 +00:00
009e71fcd9
We need to sort cleaned reads ourselves (instead of letting SAMFileWriter
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do it) because the SAM headers are often screwed up and claim to be
"unsorted". While here, I broke off the module from the SortSamIterator
in case someone else wants to use it.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@654 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 15:43:42 +00:00
c735e1f627
small javadoc cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@653 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 03:44:21 +00:00
e8b8ab5985
Added code to extend Matt's getReferenceBases out to the read walkers, so they can see the corresponding reference for each read.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@652 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 03:42:38 +00:00
4ce3feba4d
my move ended up being a copy, so this is to delete dupplicate files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@651 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 02:10:26 +00:00
898f65547e
Added code to split GenomeAnalysisTK.java into an object concerned with loading command line args, and one that runs the engines. This will allow us to run the GATK from other tools (like Matlab). Also some cleanup to seperate out the legacy traversals and the new style traversals. This is not live yet, and any modifications you need should be made to GenomeAnalysisTK.java for now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@650 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 02:07:20 +00:00
8d43ec3d7e
a fix for a situation where a chromosome on the reference file contains no reads, and doesn't align to the bam file. This came up using reference 18, which has chomosomes like chr1_random that aren't in all BAM files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@649 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 01:39:25 +00:00
ee02b61068
added support for the argument collections code
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@648 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-09 07:07:33 +00:00
742840017b
added the argument collection annotation for situations where fields in a command line args have embedded fields that should be checked for command line args
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@647 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-09 06:59:17 +00:00
55c1b688bd
Fix mediocre javadoc.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@646 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 22:31:16 +00:00
522f8b58be
Added second method for getting large sequences of the reference for use in reads traversals.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@645 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 22:18:04 +00:00
517f27f331
Added sharding strat. code that picks the right kind of shard, based on the traversal engine
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@644 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 21:55:10 +00:00
6e394490cb
Cleanup in preparation for ByLoci traversal. Also did some work minimizing unit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@643 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 21:27:54 +00:00
ee777c89de
Change the default mechanism for adding ROD bindings to the new system. TODO: create a new object type for these triplets.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@642 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 18:43:00 +00:00
3aabc144c6
Added functionality to allow for a contract between LocusWindowTraversalEngine and LocusWindowWalker which allows the Walker to act upon reads outside of the provided intervals.
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(Really, all we want to do is spit out all reads, but this allows the Walker to do other things with the reads if it wants)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@641 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 17:28:16 +00:00
de1c282e62
Reference-ordered data relies on bugs in the old command-line argument system to work. Update the ROD system to from -B track1 type1 file1 track2 type2 file2 to -B track1,type1,file1 -B track2,type2,file2.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@640 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 15:28:19 +00:00
483a58627b
More cleanup -- pushing shared functions down into the traversal engine.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@639 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 14:12:45 +00:00
7a9cfe1f75
Push reduceInit down a level so that the walker can call into it without weird casts.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@638 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 13:46:28 +00:00
a5154d99a3
Haven't heard any complaints, so I'm deleting the original implementation of TraverseByLociByReference. All TbyLbyR's will now go through the new sharding code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@637 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 13:37:00 +00:00
bae4256574
Started the process to make the GATK engine into a runnable object so we can call it from other processes. Step 1: make a configuration object that can serialize to and from an XML file. This way we can store the information everyone uses shell scripts for. Also we can now pull the list of params out of the GenomeAnalysisTK.java. More to come...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@636 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 01:25:26 +00:00
226edbdef6
Hypen-style xml output. Much sexier.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@635 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 01:04:40 +00:00
4c269b8496
Cleanup LinearMicroScheduler in preparation for TraverseByLoci inclusion.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@634 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 00:58:37 +00:00
21536df308
Change the sample XML marshalling code over to simple XML, and take out the castor lines in the ivy.xml
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@633 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 00:08:25 +00:00
7f8850a8a2
Argument validation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@631 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 20:28:56 +00:00
a3d8febbf2
Error message cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@630 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 19:31:32 +00:00
c241d386a7
Beefed up command-line usage string.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@629 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 19:08:19 +00:00
5a6892900e
fixing oddities in duplicates
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@628 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:55:45 +00:00
4a26f35caa
new default syntax
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@627 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:16:53 +00:00
283a4d1b54
Fix some special-case cleaner issues.
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We now do the same as brute force in all examples to date.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@626 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:16:35 +00:00
93211c1cd8
template for windowmaker utility -- total non-functional
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@625 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:13:03 +00:00
2204be43eb
System for traversing duplicate reads, along with a walker to compute quality scores among duplicates and a smarter method to combine quality scores across duplicates -- v1
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@624 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:06:02 +00:00
71e8f47a6c
boundQual function for capping qual values
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@623 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:04:18 +00:00
e848f34896
countOccurances of char in string and max of a list of bytes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@622 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:03:49 +00:00
5a4bb76cc3
More capabilities for the pileup
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@621 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:03:13 +00:00
89a26a7078
Utilities for handling duplicates
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@620 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 18:02:24 +00:00
4f85062004
Cleanup parsing method to make it less generic.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@619 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 16:21:17 +00:00
d725c6cf1c
Added unit tests for parsing failures that I encountered during integration testing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@618 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 14:01:54 +00:00
2f3ab53888
Oops. Arguments didn't load into applications with non-plugins (basically everything except the GATK).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@617 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 13:37:19 +00:00
4177560543
Mutually exclusive options.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@616 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 13:27:48 +00:00
752928df94
Switch to better mechanism for supplying a default.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@615 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 01:22:01 +00:00
dc944ec69b
First stage of ROD plumbing for MicroScheduler.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@614 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 23:26:21 +00:00
5136724884
Added code to the schedulers, one step closer to turning on the new reads traversals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@613 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 22:36:25 +00:00
9c0b81e946
Default flags to 'not required'.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@612 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 22:09:49 +00:00
072808858e
added COUNT_CUTOFF arg: it is nor possible to tell the code to try to realign all read piles over trains of nearby indels with at least one indel observed in COUNT_CUTOFF or more different alignments (set the arg to 1 to realign around all indels); also, some diagnostic printouts added to the output (time spent on loading the reference, time spent on scrolling through the input bam file, counts of discarded reads)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@611 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 21:59:33 +00:00
1fe8155111
Some critical fixes for cases where argument values directly abut argument names
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and for arguments with missing short names.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@610 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 21:47:34 +00:00
0aba688e6f
Added a interface that all our SAMRecord iterators should try to code to. This is in the effort to keep our code generic
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@609 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 21:40:41 +00:00
62e7e46754
Miscellaneous cleanup. Better display of help output. Better exception subtyping. More thought-out access routines.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@608 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 21:16:01 +00:00
5be75e0ae6
First version of indel cleaner walker that works on intervals
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@607 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 20:20:48 +00:00
98716138e9
Cleanup: add support for non-public fields. Track matches as state of parsing engine as well as definitions.
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Made fields of command-line argument system non-public by default.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@606 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 19:38:05 +00:00
f5eae98af2
Fixed a bug where we could ask for a read when there were none in the pool (that's a bad thing).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@605 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 18:40:55 +00:00
ef211f96b1
Remove old Apache CLI-based arg system.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@604 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 18:37:51 +00:00
521aa40baa
Bring new command-line argument parsing system live.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@603 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 18:16:11 +00:00
98f4920739
Added BCEL and some basic instrumenation code to the test library.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@602 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 17:18:23 +00:00
bfd6dfe36c
Added real-world tests and tests for conditional validation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@601 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 13:38:46 +00:00
4ac9e72739
Migrate default and GATK arguments over to new attribute system in preparation for conversion.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@600 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 23:57:48 +00:00
2ee9374975
Check for proper error output in case of boolean args with parameter specified.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@599 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 23:08:48 +00:00
b0cdba8bb3
Acting on Kiran's suggestion to make the doc tag in the @Argument annotation required.x
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@598 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 22:43:40 +00:00
ec0261275b
Lots of command line argument validation. Catches all common validation problems, including missing required arguments, invalid arguments, and several types of misplaced argument value errors.
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Still pending:
- Help system.
- Mutually exclusive arguments.
- Design includes too many classes per file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@597 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 22:08:00 +00:00
70afda12c4
Cut the test time down
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@596 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 22:05:51 +00:00
f5880109a7
Added TraverseReads test, some bug fixes discovered in the traversal test
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@594 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 20:36:00 +00:00
daa2163ee8
Made the MergingSamIterator2 peekable. This iterator is being a ducktaped together swiss army knife, the iterators could use a redo soon.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@593 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 19:15:07 +00:00
09b0b6b57d
Fixes to try and speed up unmapped read traversals. Still not nearly as fast as they should be, but the next step would be to modify samtools code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@592 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 18:17:07 +00:00
6550fe6f97
Another pass of command-line arguments. Revised parser supports all types
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of arguments that the existing parser supports, but does a poor job with
validation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@591 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-04 22:41:23 +00:00
8925df2e1e
More information from the duplicate combiner quality metrics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@590 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-04 21:51:01 +00:00
2b6466ea00
coverage calculator based on Gabor's Pilot 3 Coverage Metrics
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@589 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-04 14:18:16 +00:00
4f2ccda56a
Interface skeleton for a new command line argument parser. Nowhere near the point of being a drop-in replacement for apache cli yet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@588 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-04 00:11:42 +00:00
6e38966349
Rename some key classes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@587 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 22:01:04 +00:00
5bdf653919
Cleanup: prepare for better output handling.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@586 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 21:40:46 +00:00
fd496159a8
Added convenience functions for RefHanger
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@585 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 21:14:40 +00:00
7ed496b859
JUnit test for RefHanger
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@584 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 20:11:14 +00:00
9f5f6f9bc7
N-way parallelism. Works for small test cases. Untested for large test cases.
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-Needs more comprehensive unit testing.
-Needs some basic refactoring.
-Needs rethink of interface boundaries.
-Needs to play more nicely in the /tmp sandbox.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@583 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 19:34:09 +00:00
df88c4d6b0
Added some code to determine the on-genotype and off-genotype secondary base distributions (which, at the moment, is commented out).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@582 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 06:48:19 +00:00
e7534b292f
Optionally applies secondary base distribution priors to normal single-sample genotyper posteriors.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@581 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 06:36:32 +00:00
58c80d8d87
For on and off-genotype primary bases, optionally compute the concordance of the secondary bases to their expected distributions. Each genotype has slightly different profiles.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@580 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 06:33:48 +00:00
16467ae7cf
A better (less overflow-y) implementation of multinomialProbability().
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@579 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 06:28:16 +00:00
4f818f5c1c
Choose a random base to stick in the pileup if the 2nd-best base matches the best base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@578 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 06:27:37 +00:00
9800d09608
A more thorough test for multinomialProbability.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@577 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-01 06:27:05 +00:00
84dae06d5a
Initial version of ByDuplicates traversal, as well as a duplicate quality score estimator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@576 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 22:16:21 +00:00
ff420f5f6f
Enabled iterator() function
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@575 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 22:15:14 +00:00
12d6edfe7c
Only prints about first contig info setting
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@574 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 22:14:26 +00:00
1cc5e74435
More ways to access quality utils
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@573 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 22:12:07 +00:00
63403d32cd
Changes to the interface to the simple data source rippled out to a bunch of files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@572 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 20:35:56 +00:00
19e4e97f21
Add tag to ignore node class.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@571 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 20:27:34 +00:00
7f173af2ea
Encapsulate output tracking a bit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@570 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 15:12:13 +00:00
3bf3c21ddd
Changed the assert code in the genome loc to throw exceptions, and deleted a function no one seems to be using.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@569 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 13:54:51 +00:00
b630f2f2f1
More tables output by CovariateCounterWalker AND made CovariateCounterWalker and LogisticRecalibration aware of positive and negative strandedness of data which changes the regression output significantly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@568 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-30 01:22:50 +00:00
f7a877bfeb
Changed Sting exception from a base exception to a runtime exception. This makes it so you can throw it without the consumer having to check it, and hopefully people will be more inclined to use it.
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Please use this instead of throwing a plain runtime exception.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@567 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 22:09:41 +00:00
ba9a0b5da8
Break out some of the weird inner classes out of the HierachicalMicroScheduler.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@566 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 21:07:07 +00:00
95d10ba314
Sketch of hierarchical reduce process, with unit tests for some core classes. Requires breakout of inner classes, testing.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@565 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 20:26:16 +00:00
0a707a887b
Added ability to evaluate best + random base.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@564 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 20:05:36 +00:00
334f158e5a
added parameters for mapping quality and duplicate filters
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@563 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 18:05:34 +00:00
7de5da7065
Start getting the cleaner working in Walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@561 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 14:59:53 +00:00
4c5f640eb7
Tweak the arguments passed to the command-line arguments parser so that it fails less often for invalid arguments.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@560 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 14:36:27 +00:00
f557da0a78
Calculate interval-based statistics for Hybrid Selection
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@558 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 04:01:24 +00:00
6ecc43f385
Provide a default logger, some config settings, and some doc updates.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@557 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 02:06:05 +00:00
b836761104
removed the test cases from the bottom of this file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@556 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-28 21:50:22 +00:00
6b02248298
moved the test cases out of the GenomeAnalysisTK code and into a JUnit test case
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@555 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-28 21:49:17 +00:00
d4de68e260
added changes for the readsTraversal to accomidate design changes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@553 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-28 19:49:58 +00:00
b6874f30cb
Added changes to bounded read iterator, it now explicitly takes a MSRI2 instead of the interfaces ClosableIterator<SAMRecord>. It would be good to fix this in the future with an interface that lets you get the (possibly merged) header.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@552 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-28 17:57:54 +00:00
395aaf48b0
Added the new by reads traversal, still needs to be sewn into the micromanager code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@551 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-28 17:55:08 +00:00
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
aaron
hanna
asivache
ebanks
depristo
andrewk
kcibul
jmaguire
kiran