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Commits on Oct 26, 2017

• more stringent recognition of transcripts (only exon-based entities are loaded)

  gpertea

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Commits on Oct 25, 2017

• sync gclib updates

  gpertea

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  6ea88d3

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• updated prepDE with some usability changes

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Commits on Aug 25, 2017

• enforce signed char (issue #138)

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Commits on Jul 12, 2017

• Merge pull request #128 from nsoranzo/patch-1

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• Merge pull request #133 from razsultana/patch-1

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Commits on Jul 8, 2017

• Update README.md

  razsultana

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  ef98b3f

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Commits on Jun 1, 2017

• Fix default values for 2 merge options

  nsoranzo

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  2ba0f4c

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Commits on Apr 6, 2017

• fixed unnecessary error when gene_id is missing in GTF

  gpertea

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Commits on Mar 27, 2017

• updated prep_*.sh files

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  2678e4e

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• patch release v1.3.3b

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Commits on Mar 26, 2017

• fix merge of transcripts on opposite strands (issues #105, #100)

  gpertea

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  90fc13f

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• fixed glitch that allowed duplicate GFF attributes

  gpertea

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  f556e32

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• redesigned GTF parsing to fix GENCODE v20- regression

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  0731d0a

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Commits on Feb 15, 2017

• v1.3.3: fixed TPM and coverage calculation for -G

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  ea8c948

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Commits on Jan 29, 2017

• removed wasteful redundant check when adding exon feature

  gpertea

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  5e339d7

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• v1.3.1d: fixed too permissive GFF parsing bug in gclib

  gpertea

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  ba1566b

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Commits on Jan 27, 2017

• fixed dumb crash in GTF parsing

  gpertea

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Commits on Jan 24, 2017

• fixed ordering comparator bug which caused a crash in some situations

  gpertea

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Commits on Jan 18, 2017

• Merge branch 'devel'

  gpertea

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  4212eaf

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• parse gene_name from GTF exons too

  gpertea

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  bea2b93

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• turn off GFF debug

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  09dcd86

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• removed useless GFF warning

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Commits on Jan 17, 2017

• WIP: partial fix for _gene_segment entries

  gpertea

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  6709ae7

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• WIP: adjust GTF parsing

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Commits on Dec 23, 2016

• sync gclib/GFastaIndex fix

  gpertea

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  f78c9fa

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• added stranded library options; fixed one base exon crash; fixed duplicate printing of transcripts

  gpertea

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  a6e318d

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Commits on Nov 30, 2016

• fixed GFF3 parsing bug caused by the overzealous requirement of gene parents to encompass all their transcripts coordinates

  gpertea

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Commits on Nov 29, 2016

• added prepDE.py script

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Commits on Nov 22, 2016

• re-fix of samtools aux tag parsing bug using htslib code

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  7e48e3c

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• fixed samtools old bug with float tags

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Commits on Nov 16, 2016

• finally found the GBitVec error cause, fixed

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Commits on Nov 15, 2016

• added GBamRecord::tag_float()

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  8d27659

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• bug fix for an index out of range error in v1.3.1

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Commits on Nov 12, 2016

• Merge branch 'devel'

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