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View685d60e
work towards supporting new bam_tally; drops quality info (now cutoff based), adds xs/nm/del and codon-level countsMichael Lawrence authored on 13/11/2015 21:50:11 |
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Viewf18ff85
more robust check for empty read pos breaksMichael Lawrence authored on 02/11/2015 22:42:05 |
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Viewbfeb9ea
fix forwarding args to TallyIITMichael Lawrence authored on 02/11/2015 21:40:00 |
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View8418591
resurrect improvements that we reverted before the April release, expect breakage for a whileMichael Lawrence authored on 28/10/2015 18:51:00 |
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Viewd5ed124
Reverted to r101133, along with NAMESPACE fixesMichael Lawrence authored on 14/04/2015 21:40:44 |
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Viewc8fd96e
Recent work towards supporting the new features... will revert back to a stable version immediately...Michael Lawrence authored on 14/04/2015 21:32:10 |
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View085e7d8
fix change of cds_iit to exon_iitGabriel Becker authored on 13/08/2014 20:26:10 |
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Viewc78be69
add codon tally support. No vbump yetGabriel Becker authored on 11/08/2014 23:42:48 |
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View6f40570
fix typo in VCF FORMAT header for read.pos.mean.refMichael Lawrence authored on 25/07/2014 20:15:30 |
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Viewab8835c
fix seqinfo merging in variantSummaryMichael Lawrence authored on 16/05/2014 21:33:43 |
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Viewf5e63d3
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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View9f0e3a7
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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View96cf993
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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View6d5d75f
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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View6a7e619
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 |