Mark DePristo
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dc9b351b5e
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Meaningful error message when an IntervalArg file fails to parse correctly
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2011-11-10 17:10:26 -05:00 |
Eric Banks
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cafc245a43
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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?
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2011-10-27 23:54:28 -04:00 |
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Eric Banks
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4a7e6fee3f
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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.
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2011-10-27 13:38:08 -04:00 |
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Eric Banks
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b6ce6ed3f8
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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.
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2011-10-26 15:42:53 -04:00 |
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Eric Banks
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9424e8b2ca
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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.
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2011-10-26 14:11:49 -04:00 |