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Commits on Sep 7, 2016

• v1.3.0 merge

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• v1.3.0 with improved abundance estimation algorithm; UCSC GTF parsing fix

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  ae6d0dd

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Commits on Jul 25, 2016

• v1.2.4 fixes

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Commits on Jul 13, 2016

• fixed mismatched gffnames_unref()

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  d310ec3

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• Merge branch 'devel'

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  04ebedb

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• fixed Gencode GTF parsing (again)

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Commits on Jun 30, 2016

• Merge branch 'devel'

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  de78e82

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Commits on Jun 29, 2016

• fixed serious GLineReader bug

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  6c4f6a4

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Commits on Jun 14, 2016

• fixing gene parsing issues (Gencode, etc.)

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Commits on Jun 9, 2016

• Merge branch 'devel'

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  f377a4e

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• fixed terrible,old bug in GStr::tr() which messed up tempy file name without -o

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Commits on May 25, 2016

• Merge branch 'devel'

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  6cd2c55

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• fix for another rare GBitVec index error; parentless CDS/exon features in bacteria are now seen as transcripts

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  2eb0613

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Commits on May 12, 2016

• merge branch 'devel'

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• added --bam option for stdin streaming; now skipping invalid mappings (mapped_len<10 or pos<1)

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Commits on May 11, 2016

• Merge branch 'devel'

  Show description for cf0681b
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• restored coord + hit index suffix for hashread

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  e83e093

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• adding per-thread stack size control

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  23bd524

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• Update README.md

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  67f95c0

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• fixed a few typos, one affecting bundledist default

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  ef43666

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• updated README

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  2a0f9f3

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• fixed new recursive mkdir() procedure

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  50d2eb0

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• removed _POSIX_SOURCE #define which can cause problems on OS X

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  4ef0259

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• fixed in_bundle flag for e_only when no reads are added to a bundle (no exon overlap)

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  c9c2f50

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• retained intron option, collapse of reads for merge option

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  6d34344

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• reworked Gmkdir() fixes

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  e019bb2

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• --merge supporting a list of *.bam files

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  28e42ed

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• let GffReader close the guides file

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  9c91a96

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• fixed long standing open file leak in GffReader

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• v1.2.2 fixes, bundling guides that may overlap another guide before the first read in the bundle

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• writing unbundled reference genes to the -A file

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• unbundled guides are written to the output GTF for -e and --merge; unbundled genes to the -A file

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• prep v1.2.2: added chromosome/reference name to gene abundance file; if a neutral group is within bundledist of a stranded group it is merged with the stranded group

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  6957667

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• keep transcript data uptr around for all guides

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  063011d

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• fixed gene&transcript numbering issues for some cases;

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