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Commits on Oct 13, 2016

• Update GFF3_utils.pm

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  Imoteph

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Commits on Oct 6, 2016

• Update gmap Flag (gmap Version 2016-09-23)

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Commits on Dec 7, 2015

• update to recognize latest Trinity accession values

  brianjohnhaas

  committed
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Commits on Aug 11, 2015

• Merge pull request PASApipeline#12 from mimarsh2/mysqlSocket

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  brianjohnhaas

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Commits on Aug 10, 2015

• Socket usage documentation

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  mimarsh2

  committed
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• Allow mysql connection through socket

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  mimarsh2

  committed
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Commits on Jun 13, 2015

• ok

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  brianjohnhaas

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• the Error, have 3prime partial protein when 3prime partials werent allowed! message was due to annotations or transcript structures being imported with coordinates that extend beyond the length of …

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Commits on Jun 11, 2015

• ok

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• update

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  committed
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Commits on May 8, 2015

• if -r mode, try to remove existing db but dont fail if it does not exist

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  committed
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Commits on Apr 28, 2015

• added the process ID into the inx filename to better provide uniqueness when the target gff3 file is being shared among several parallel proesses

  brianjohnhaas

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Commits on Apr 22, 2015

• treat transcript features identically to mRNA features in gff3

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Commits on Apr 4, 2015

• renamed

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  committed
  68bf080

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• deprecate

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Commits on Mar 30, 2015

• bugfix.. got it this time.

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• store gene id not trans id as the gene_id att, bugfix

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Commits on Mar 27, 2015

• ok

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• include gff3-alignment to gtf conversion util

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  committed
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Commits on Mar 13, 2015

• dont need the optimize tables script

  brianjohnhaas

  committed
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Commits on Feb 23, 2015

• Merge pull request PASApipeline#2 from eernst/patch-1

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• Support Trinity 2.0.0+ style accessions

  eernst

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Commits on Feb 20, 2015

• make it clear the error message coming from mysql

  brianjohnhaas

  committed
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• use blat and gmap

  brianjohnhaas

  committed
  7309955

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• use update gmap script

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  committed
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Commits on Feb 19, 2015

• added table optimizations to workflow

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  committed
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• add

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Commits on Feb 13, 2015

• update

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  da8f6b0

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• get rid of forced index

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Commits on Feb 10, 2015

• initial import

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• Initial commit

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