78343be52c
At some time in the recent past, we lost our ability to process the '-L all'
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argument. Brought it back, and added an integrationtest to make sure it
stays around.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4390 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-30 15:58:43 +00:00
4d0ff336c2
Missed update input
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4269 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 15:46:13 +00:00
7880863eb7
Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4267 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 15:07:38 +00:00
7ad8fbdd5a
Moved GATKException to exceptions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4266 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 14:47:19 +00:00
40e6179911
Penultimate step in exception system overhaul. UserError is now UserException. This class should be used for all communication with the USER for problems with their inputs. Engine now validates sequence dictionaries for compatibility, detecting not only lack of overlap but now inconsistent headers (b36 ref with v37 BAM, for example) as well as ref / bam order inconsistency. New -U option to allow users to tolerate dangerous seq dict issues. WalkerTest system now supports testing for exceptions (see email and wiki for docs). Tests for vcf and bam vs. ref incompatibility. Waiting on Tribble seq dict improvements to detect b36 VCF with b37 ref (currently cannot tell this is wrong.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4258 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 14:02:43 +00:00
30178c05c5
providing a way to specify how you'd like -BTI combined with your -L options; set BTIMR to either UNION (default) or INTERSECTION.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3983 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-09 14:00:52 +00:00
671ac00748
A simple utility class that implements a merging Iterator<GenomeLoc> built over an interval or bed file (this is NOT a rod, but rather a direct line-by-line file reader that converts strings to genome locs on the fly and merges overlapping intervals)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3546 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-14 15:54:37 +00:00
hanna
depristo
aaron
asivache