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commit 3afccf9e86ec90e9525df476bc3037c6491de683 1 parent 6e9d928
Brian Osborne bosborne authored
Showing with 3 additions and 46 deletions.
  1. +0 −1  lib/Bio/DB/ESoap.pm
  2. +1 −0  lib/Bio/Tools/Run/Alignment/Amap.pm
  3. +0 −1  lib/Bio/Tools/Run/Alignment/Clustalw.pm
  4. +0 −1  lib/Bio/Tools/Run/Alignment/DBA.pm
  5. +0 −1  lib/Bio/Tools/Run/Alignment/Exonerate.pm
  6. +0 −1  lib/Bio/Tools/Run/Alignment/Gmap.pm
  7. +0 −1  lib/Bio/Tools/Run/Alignment/Kalign.pm
  8. +0 −1  lib/Bio/Tools/Run/Alignment/MAFFT.pm
  9. +0 −1  lib/Bio/Tools/Run/Alignment/MSAProbs.pm
  10. +0 −1  lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
  11. +0 −1  lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
  12. +0 −1  lib/Bio/Tools/Run/Alignment/TCoffee.pm
  13. +0 −1  lib/Bio/Tools/Run/Analysis.pm
  14. +0 −1  lib/Bio/Tools/Run/AnalysisFactory.pm
  15. +0 −1  lib/Bio/Tools/Run/AssemblerBase.pm
  16. +0 −1  lib/Bio/Tools/Run/BEDTools.pm
  17. +2 −3 lib/Bio/Tools/Run/BWA.pm
  18. +0 −1  lib/Bio/Tools/Run/BlastPlus.pm
  19. +0 −1  lib/Bio/Tools/Run/Bowtie.pm
  20. +0 −1  lib/Bio/Tools/Run/Cap3.pm
  21. +0 −1  lib/Bio/Tools/Run/EMBOSSApplication.pm
  22. +0 −1  lib/Bio/Tools/Run/EMBOSSacd.pm
  23. +0 −1  lib/Bio/Tools/Run/ERPIN.pm
  24. +0 −1  lib/Bio/Tools/Run/Ensembl.pm
  25. +0 −1  lib/Bio/Tools/Run/Eponine.pm
  26. +0 −1  lib/Bio/Tools/Run/FootPrinter.pm
  27. +0 −1  lib/Bio/Tools/Run/Genemark.pm
  28. +0 −1  lib/Bio/Tools/Run/Genewise.pm
  29. +0 −1  lib/Bio/Tools/Run/Infernal.pm
  30. +0 −1  lib/Bio/Tools/Run/MCS.pm
  31. +0 −1  lib/Bio/Tools/Run/Maq.pm
  32. +0 −1  lib/Bio/Tools/Run/Match.pm
  33. +0 −1  lib/Bio/Tools/Run/Mdust.pm
  34. +0 −1  lib/Bio/Tools/Run/Meme.pm
  35. +0 −1  lib/Bio/Tools/Run/Phrap.pm
  36. +0 −1  lib/Bio/Tools/Run/Primer3.pm
  37. +0 −1  lib/Bio/Tools/Run/Profile.pm
  38. +0 −1  lib/Bio/Tools/Run/Promoterwise.pm
  39. +0 −1  lib/Bio/Tools/Run/RNAMotif.pm
  40. +0 −1  lib/Bio/Tools/Run/RepeatMasker.pm
  41. +0 −1  lib/Bio/Tools/Run/Samtools.pm
  42. +0 −1  lib/Bio/Tools/Run/Samtools/Config.pm
  43. +0 −1  lib/Bio/Tools/Run/Seg.pm
  44. +0 −1  lib/Bio/Tools/Run/Simprot.pm
  45. +0 −1  lib/Bio/Tools/Run/StandAloneBlastPlus.pm
1  lib/Bio/DB/ESoap.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::DB::ESoap
#
1  lib/Bio/Tools/Run/Alignment/Amap.pm
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@@ -1,3 +1,4 @@
+#
# BioPerl module for Bio::Tools::Run::Alignment::Amap
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
1  lib/Bio/Tools/Run/Alignment/Clustalw.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Run::Alignment::Clustalw
#
1  lib/Bio/Tools/Run/Alignment/DBA.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Run::Alignment::DBA
#
1  lib/Bio/Tools/Run/Alignment/Exonerate.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
1  lib/Bio/Tools/Run/Alignment/Gmap.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Run::Alignment::Gmap
#
1  lib/Bio/Tools/Run/Alignment/Kalign.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Run::Alignment::Kalign
#
1  lib/Bio/Tools/Run/Alignment/MAFFT.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Run::Alignment::MAFFT
#
1  lib/Bio/Tools/Run/Alignment/MSAProbs.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Run::Alignment::MSAProbs
#
1  lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
View
@@ -1,4 +1,3 @@
-# $Id: Pal2Nal.pm,v 1.3 2007/05/25 10:14:55 sendu Exp $
#
# BioPerl module for Bio::Tools::Run::Alignment::Pal2Nal
#
1  lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
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@@ -1,4 +1,3 @@
-# $Id$
#StandAloneFasta.pm v1.00 2002/11/01
#
#Bioperl module for Bio::Tools::Run::Alignment::StandAloneFasta
1  lib/Bio/Tools/Run/Alignment/TCoffee.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Run::Alignment::TCoffee
#
1  lib/Bio/Tools/Run/Analysis.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Run::Analysis
#
1  lib/Bio/Tools/Run/AnalysisFactory.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Run::AnalysisFactory
#
1  lib/Bio/Tools/Run/AssemblerBase.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Run::AssemblerBase
#
1  lib/Bio/Tools/Run/BEDTools.pm
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@@ -1,4 +1,3 @@
-# $Id: BEDTools.pm kortsch $
#
# BioPerl module for Bio::Tools::Run::BEDTools
#
5 lib/Bio/Tools/Run/BWA.pm
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@@ -1,6 +1,3 @@
-# $Id$
-package Bio::Tools::Run::BWA;
-use strict;
#
# BioPerl module for Bio::Tools::Run::BWA
#
@@ -171,6 +168,8 @@ Internal methods are usually preceded with a _
# Let the code begin...
+package Bio::Tools::Run::BWA;
+use strict;
use IPC::Run;
our $HAVE_IO_UNCOMPRESS;
1  lib/Bio/Tools/Run/BlastPlus.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Run::BlastPlus
#
1  lib/Bio/Tools/Run/Bowtie.pm
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@@ -1,4 +1,3 @@
-# $Id: Bowtie.pm kortsch $
#
# BioPerl module for Bio::Tools::Run::Bowtie
#
1  lib/Bio/Tools/Run/Cap3.pm
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@@ -1,4 +1,3 @@
-# $Id$
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
1  lib/Bio/Tools/Run/EMBOSSApplication.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Run::EMBOSSApplication
#
1  lib/Bio/Tools/Run/EMBOSSacd.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Run::EMBOSSacd
#
1  lib/Bio/Tools/Run/ERPIN.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Run::ERPIN
#
1  lib/Bio/Tools/Run/Ensembl.pm
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@@ -1,4 +1,3 @@
-# $Id: Ensembl.pm,v 1.6 2006/07/17 14:16:53 sendu Exp $
#
# BioPerl module for Bio::Tools::Run::Ensembl
#
1  lib/Bio/Tools/Run/Eponine.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
1  lib/Bio/Tools/Run/FootPrinter.pm
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@@ -1,4 +1,3 @@
-# $Id$
# BioPerl module for FootPrinter
#
# Copyright Shawn Hoon
1  lib/Bio/Tools/Run/Genemark.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Run::Genemark
#
1  lib/Bio/Tools/Run/Genewise.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
1  lib/Bio/Tools/Run/Infernal.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# You may distribute this module under the same terms as perl itself
#
1  lib/Bio/Tools/Run/MCS.pm
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@@ -1,4 +1,3 @@
-# $Id: MCS.pm,v 1.3 2007/05/25 10:14:55 sendu Exp $
#
# BioPerl module for Bio::Tools::Run::MCS
#
1  lib/Bio/Tools/Run/Maq.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Run::Maq
#
1  lib/Bio/Tools/Run/Match.pm
View
@@ -1,4 +1,3 @@
-# $Id: Match.pm,v 1.3 2007/05/25 10:14:55 sendu Exp $
#
# BioPerl module for Bio::Tools::Run::Match
#
1  lib/Bio/Tools/Run/Mdust.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Mdust
#
1  lib/Bio/Tools/Run/Meme.pm
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@@ -1,4 +1,3 @@
-# $Id: Meme.pm,v 1.25 2006/07/04 22:23:31 mauricio Exp $
# BioPerl module for Meme
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
1  lib/Bio/Tools/Run/Phrap.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# Phrap wraper module
#
1  lib/Bio/Tools/Run/Primer3.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# This is the original copyright statement. I have relied on Chad's module
# extensively for this module.
1  lib/Bio/Tools/Run/Profile.pm
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@@ -1,4 +1,3 @@
-# $Id$
# BioPerl module for Profile
# Copyright Balamurugan Kumarasamy
#
1  lib/Bio/Tools/Run/Promoterwise.pm
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@@ -1,4 +1,3 @@
-# $Id: Promoterwise.pm,
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
1  lib/Bio/Tools/Run/RNAMotif.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Run::RNAMotif
#
1  lib/Bio/Tools/Run/RepeatMasker.pm
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@@ -1,4 +1,3 @@
-# $Id$
# BioPerl module for RepeatMasker
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
1  lib/Bio/Tools/Run/Samtools.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Run::Samtools
#
1  lib/Bio/Tools/Run/Samtools/Config.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Run::Samtools::Config
#
1  lib/Bio/Tools/Run/Seg.pm
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@@ -1,4 +1,3 @@
-# $Id$
# Copyright Balamurugan Kumarasamy
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
1  lib/Bio/Tools/Run/Simprot.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Run::Simprot
#
1  lib/Bio/Tools/Run/StandAloneBlastPlus.pm
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@@ -1,4 +1,3 @@
-# $Id$
#
# BioPerl module for Bio::Tools::Run::StandAloneBlastPlus
#
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