e77dfe9983
Allow script to be easily modified to support different platforms.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@955 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 16:06:57 +00:00
7fa84ea157
10x speedup of recalibration walker
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@954 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 15:39:40 +00:00
a62bc6b05d
fixed some documentation and attached a correct license
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@953 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 14:44:27 +00:00
bf6190b471
cleaned up the PrintReadsWalker, and added a lot of documentation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@952 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 14:28:32 +00:00
b45b1d5f2b
border case bug fixes
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@951 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 04:33:15 +00:00
fecba2cae5
Disabled option to show secondary quals as the definition has changed to conform to the spec and thus this printout is non-sensical.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@950 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 03:21:14 +00:00
e7f222108d
More accessors. Can compute the sum of the quality scores in the read (useful for sorting) and can return a subset of itself.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@948 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 01:02:48 +00:00
6506504a60
Updates after seeing a certain number of reads, not a certain number of bases.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@947 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 01:01:36 +00:00
65d0675a4e
Some changes regarding what to do when a cycle is completely busted.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@946 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 01:01:13 +00:00
0bd78d72d7
Some changes regarding what to do when a cycle is completely busted.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@945 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 01:00:33 +00:00
af0b03a257
Added tests for mostFrequentBaseFraction() and reverseComplementString()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@944 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 00:53:45 +00:00
681e67c72c
Added some methods to generate random bases or random base indexes, optionally disallowing the generation of a specified base or base index.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@943 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 00:47:54 +00:00
13eb868536
helper class. array-like random access and fast shift. good for sliding windows (e.g. keeping coverage over last 100 bases while sliding along the reference)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@942 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 00:11:57 +00:00
3d6e738a60
still under development. does not genotype yet, but walks and talks (counts overal coverage and indel variant occurences at every reference position
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@941 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-09 00:10:31 +00:00
58f7ae8628
better filtering, plus deal with case where user doesn't input maxlength
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@939 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-08 18:44:29 +00:00
ce431b5d2d
added hashCode()
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@937 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-08 16:52:02 +00:00
b4ef16ced2
extractIndels() now should deal correctly with soft- and hard-clipped bases
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@936 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-08 16:04:49 +00:00
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
hanna
depristo
aaron
ebanks
kiran
asivache
andrewk
kcibul
jmaguire