df9133c90b
the doc on File.length states it returns 0L if it doesn't exist, added a check to make sure it exists (and length < 1)
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1450 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-21 05:55:17 +00:00
cd711d7697
Added detection of interval files with zero length to the GATK, and removed it from the interval merger walker: this was a critical blocking emergency issue for Eric.
...
also fixed some verbage in the GAEngine.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1449 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-21 05:35:49 +00:00
129ad97ce5
performance improvement to GenomeLocParser -- moved regex pattern compile out of local field
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1272 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-17 02:56:25 +00:00
e106cf73d8
A quick change to provide more verbose output.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1197 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 19:08:19 +00:00
7462f3f344
Bug in setContig() fixed: sequence dictionary's .getSequences().contains() and .getSequences().indexOf() do NOT work when applied to contig names (Strings), since getSequences() returns a list of SAMSequenceRecord's; changed to querying the dictionary directly for specified contig name
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1147 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-01 20:50:09 +00:00
f5cba5a6bb
Fixed genome loc to be immutable, the only way to now change it's values is through the GenomeLocParser.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1132 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-30 19:17:24 +00:00
5289230eb8
Version 0.2.1 (released) of the TableRecalibrator
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1108 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 22:50:55 +00:00
61ce4e5983
quick doc change
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1086 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-24 16:35:46 +00:00
bcb64d92e9
Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1069 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-22 14:39:41 +00:00
aaron
kcibul
asivache
depristo