git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@75206 bc3139a8-67e5-0310-9ffc-ced21a209358
Michael Lawrence authored on 02/04/2013 22:39:12
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+CHANGES IN VERSION 1.2.0 |
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+----------------------- |
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+ |
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+NEW FEATURES |
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+ |
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+ o New method getSeq,GmapGenome retrieves sequence from a |
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+ GmapGenome index. This also supports a coercion to DNAStringSet |
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+ and thus easy export to FASTA via rtracklayer. |
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+ |
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+ o bam_tally gains an ignore_duplicates argument for ignoring BAM |
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+ records flagged as PCR/optical duplicates. |
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+ |
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+ o Read position mean and variance are now output by bam_tally. |
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+ |
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+USER-VISIBLE CHANGES |
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+ |
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+ o GMAP has been updated to the July '12 version (yes, this is old). |
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+ |
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+ o GSTRUCT (bamtally) updated to trunk as of 3/22/13. |
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+ |
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+BUG FIXES |
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+ |
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+ o asBam,GsnapOutput now actually works. |
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+ |
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+CHANGES IN VERSION 1.0.0 |
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+----------------------- |
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+ |
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+Initial release |
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+ |
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+(start date: 12 September, 2012) |