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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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+    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)