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add NEWS for release

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@88834 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 11/04/2014 20:23:34
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  • NEWS index c66813a..cfdc00b 100644
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+CHANGES IN VERSION 1.6.0
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+-----------------------
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+
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+NEW FEATURES
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+
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+    o Add median distance from nearest end (MDFNE) statistics to output
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+      of variantSummary.
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+
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+    o Updated GSNAP, which is orders of magnitude faster than the
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+      previous version, brings many fixes and offers many new
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+      features. One new feature is the clip_overlap argument, which
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+      clips overlapping ends of read pairs (important for variant
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+      calling).
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+
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+    o Updated bam_tally, which is faster and includes support for
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+      counting in soft-clipped regions.
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+    
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+USER-VISIBLE CHANGES
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+
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+    o Changes to tallyVariant statistics: drop the unique read
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+      position counts; renamed count.pos/count.neg to
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+      count.plus/count.minus (way better names)
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+
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+    o tallyVariants does a better job of carrying over the Seqinfo
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+      from the BAM file.
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+    
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 CHANGES IN VERSION 1.4.0
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 -----------------------
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