dc6a9ca196
Pooling resources to lower memory consumption.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@962 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 13:39:32 +00:00
3adb4239e4
Same as regular Pileup, but also allows you to see flanking region around locus. This will be useful in determining that some SNPs are spurious due to being at the ends of homopolymer regions.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@959 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 08:19:31 +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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
hanna
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