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View f053c5f
general cleanup and fixes, doc updatesMichael Lawrence authored on 03/12/2015 21:11:09 |
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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 976c80b
update docs to reflect that the read length is no longer guessedMichael Lawrence authored on 14/04/2014 20:05:59 |
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View 6ff8fc3
doc updatesMichael Lawrence authored on 10/04/2014 19:40:59 |
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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 0c27085
doc updates/fixesMichael Lawrence authored on 14/10/2013 18:52:22 |
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View 59c3684
Refactor bam_tally, so that bam_tally returns a TallyIIT object, which is then summarized via summarizeVariants; this allows computing tallies once and summarizing them in different ways (like maybe get the coverage). The summarizeVariants function yields a VRanges.Michael Lawrence authored on 14/07/2013 00:43:43 |
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View 1650977
Make 'genome' a BamTallyParam slot, instead of a bam_tally argument. This is consistent with GsnapParam. Also, rename 'high_quality_cutoff' to 'high_base_quality'.Michael Lawrence authored on 17/08/2012 20:19:50 |
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View b22faf0
renaming gmapR2 to gmapR: it lives againMichael Lawrence authored on 02/08/2012 22:24:24 |