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View 60982df
some internal cleanup in BamTallyParamMichael Lawrence authored on 13/10/2014 18:07:30 |
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View 277f5cf
GsnapOutputList now uses the internal list constructor from S4Vectors (instead of IRanges)Michael Lawrence authored on 11/10/2014 20:33:08 |
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View 555225f
allow genomes to be built from any sequence file supported by rtracklayerMichael Lawrence authored on 11/10/2014 18:17:31 |
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View 9aca6bd
generalize TP53Genome to GeneGenome, which takes a character vector of gene namesMichael Lawrence authored on 05/09/2014 21:50:22 |
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View cfb01d1
some fiddling, disable maintainer mode, vbumpGabriel Becker authored on 14/08/2014 20:39:03 |
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View 085e7d8
fix change of cds_iit to exon_iitGabriel Becker authored on 13/08/2014 20:26:10 |
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View c78be69
add codon tally support. No vbump yetGabriel Becker authored on 11/08/2014 23:42:48 |
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View c0cce6c
follow renaming of TranscriptDb class -> TxDbHerve Pages authored on 28/07/2014 23:15:59 |
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View 6f40570
fix typo in VCF FORMAT header for read.pos.mean.refMichael Lawrence authored on 25/07/2014 20:15:30 |
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View ab8835c
fix seqinfo merging in variantSummaryMichael Lawrence authored on 16/05/2014 21:33:43 |
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View f5e63d3
update to new bam_tally with support for XS counting, which we now support via BamTallyParam@count_xs.Michael Lawrence authored on 13/05/2014 02:04:05 |
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View 3b5cad5
add internal function for getting transcripts on the TP53 genomeMichael Lawrence authored on 13/05/2014 02:02:31 |
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View 9f0e3a7
bam_tally has reworked memory management to avoid memory "leaks" that seem to happen on our clusterMichael Lawrence authored on 05/05/2014 21:02:45 |
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View 96cf993
re-add counting of unique read positions (convenient when dupes are not marked) and fix an uninitialized value (param.cycle_breaks) detected by valgrindMichael Lawrence authored on 02/05/2014 12:51:58 |
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View 6d5d75f
add support for the noncovered argument; tells bam_tally to report even those positions that have no coverageMichael Lawrence authored on 30/04/2014 17:05:27 |