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
aaron
hanna
asivache
ebanks
depristo
andrewk
kcibul