2 Commits (b39fcb1bea1477ff08a31eaa3eed71fe2a970be5)

Author	SHA1	Message	Date
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