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9 Commits (58c470a6c5a23d626b582d89dc83724a42d4d2c1)

Author SHA1 Message Date
Eric Banks 337ff7887a When constructing VariantContexts from symbolic alleles, check for the END tag in the INFO field; if present, set the stop position of the VC accordingly. Added integration test to ensure that this is working properly for use with -L intervals. 2012-04-04 10:57:05 -04:00
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