gatk-3.8

Commit Graph

Author	SHA1	Message	Date
Mark DePristo	4d9582de77	More general catching of Exceptions in interval reading to throw MalformedFile exception in all cases -- Now throws UserException no matter what happens during the reading of the intervals file.	2012-02-27 14:02:26 -05:00
David Roazen	e5b85f0a78	A toString() method for IntervalBindings Necessary since we're currently writing things like this to our VCF headers: intervals=[org.broadinstitute.sting.commandline.IntervalBinding@4ce66f56]	2011-11-23 11:56:12 -05:00
David Roazen	1296dd41be	Removing the legacy -L "interval1;interval2" syntax This syntax predates the ability to have multiple -L arguments, is inconsistent with the syntax of all other GATK arguments, requires quoting to avoid interpretation by the shell, and was causing problems in Queue. A UserException is now thrown if someone tries to use this syntax.	2011-11-21 13:18:53 -05:00
Mark DePristo	dc9b351b5e	Meaningful error message when an IntervalArg file fails to parse correctly	2011-11-10 17:10:26 -05:00
Eric Banks	cafc245a43	For some reason, a class of Codecs (including TableCodec) require that a GenomeLocParser be passed in to do the position processing. Why can't they just return a Feature with chr, start, stop? Isn't that the right thing?	2011-10-27 23:54:28 -04:00
Eric Banks	4a7e6fee3f	Remove support for BED file interval parsing in the GATK; it should all go through Tribble now. IndelRealigner no longer supports unordered interval input (which shouldn't have been used anyways). Temporarily commenting out serialization of arguments so that tests pass; this whole piece will be deleted soon anyways.	2011-10-27 13:38:08 -04:00
Eric Banks	b6ce6ed3f8	Go around the ROD system for now so that we can just call decodeLoc() for efficiency. Noted that we should go through the ROD system once it gets cleaned up. This means that currently gzipped files are not supported with -L.	2011-10-26 15:42:53 -04:00
Eric Banks	9424e8b2ca	Initial working version of new interval system in which the argument for -L (and -XL) is allowed to be a rod file (e.g. VCF). Old samtools-style intervals still behave as before. BTI is no longer supported. The merging (union or intersection) of intervals is now consistently applied to all -L (or -XL) intervals, which is nice. More testing needed.	2011-10-26 14:11:49 -04:00

8 Commits (4d9582de777f3f9c9543ed1102e6da7bee2c95e9)