git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@88834 bc3139a8-67e5-0310-9ffc-ced21a209358
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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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3 | 29 |
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