git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@69328 bc3139a8-67e5-0310-9ffc-ced21a209358
Michael Lawrence authored on 11/09/2012 18:50:23
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@@ -10,7 +10,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read |
| 10 | 10 |
to work with GMAP and GSNAP from within R. In addition, it provides |
| 11 | 11 |
methods to tally alignment results on a per-nucleotide basis using |
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the bam_tally tool. |
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-Version: 0.99.16 |
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+Version: 0.99.17 |
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Depends: R (>= 2.15.0), methods, GenomicRanges |
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Imports: IRanges, Rsamtools (>= 1.7.4), rtracklayer (>= 1.17.15), GenomicRanges, |
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GenomicFeatures, Biostrings, VariantAnnotation, tools, Biobase |
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@@ -82,7 +82,7 @@ setMethod("gsnap", c("character", "characterORNULL", "GsnapParam"),
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gmap_mode = "pairsearch,terminal,improve", |
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trigger_score_for_gmap = 5L, max_gmap_pairsearch = 3L, |
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max_gmap_improvement = 3L, microexon_spliceprob = 0.90, |
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- novelsplicing = FALSE, splicingdir = NULL, |
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+ novelsplicing = 0L, splicingdir = NULL, |
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use_splicing = NULL, ambig_splice_noclip = FALSE, |
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localsplicedist = 200000L, |
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local_splice_penalty = 0L, distant_splice_penalty = 3L, |