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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 |
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View f7ab666
resync with stuff moving from IRanges to S4VectorsHerve Pages authored on 18/04/2014 15:04:25 |
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View 6a7e619
disable read length guessing; just expect the user to provide it when they need the statistics that depend on itMichael Lawrence authored on 14/04/2014 19:50:15 |
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View 30f3bfd
drop the unique read position counts; renamed count.pos/count.neg to count.plus/count.minus (way better names)Michael Lawrence authored on 04/04/2014 13:36:22 |
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View ae7cf39
bring back the unique read position count, and mean/variance of read positionsMichael Lawrence authored on 04/04/2014 13:16:32 |
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View 17db5e7
update GSTRUCT (bam_tally); add include_soft_clip parameter for counting over soft clips of a given max length (more accurate allele frequency)Michael Lawrence authored on 02/04/2014 22:03:40 |
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View ed089f7
ensure that seqlevel ordering from genome is preserved in resultMichael Lawrence authored on 02/04/2014 21:12:52 |
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View 0fd1d01
be robust to different seqlevel orderings when merging Seqinfo from GmapGenome and BamFileMichael Lawrence authored on 02/04/2014 20:54:46 |
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View 0be2bfb
cleanup gmap_build interface, add 'circular' support (automatically derived from BSgenome) and turn off chromosome sorting by defaultMichael Lawrence authored on 02/04/2014 12:59:22 |
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View fa1974f
tweak consistency checks to allow NA values (when variant_strand=0)Michael Lawrence authored on 02/04/2014 12:58:36 |