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View c3db7e3
support new version of bam_tallyMichael Lawrence authored on 12/06/2019 22:48:54 |
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View c087114
follow renaming of RangesList class -> IntegerRangesList in IRanges 2.13.12Hervé Pagès authored on 22/01/2018 00:24:43 |
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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 2debb80
fix naming of exon_iit argumentMichael Lawrence authored on 11/10/2014 20:33:34 |
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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 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 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 0c27085
doc updates/fixesMichael Lawrence authored on 14/10/2013 18:52:22 |
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View 4d5cc80
update to latest gstruct; brings faster bam_tally (for high coverage regions) and read-group filtering support in bam_tallyMichael Lawrence authored on 20/09/2013 02:05:42 |
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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 df903e0
Add ignore_duplicate argument to BamTallyParamMichael Lawrence authored on 26/03/2013 21:40:15 |
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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 |