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commit 3afccf9e86ec90e9525df476bc3037c6491de683 1 parent 6e9d928
bosborne authored February 08, 2012

Showing 45 changed files with 3 additions and 46 deletions. Show diff stats Hide diff stats

  1. 1  lib/Bio/DB/ESoap.pm
  2. 1  lib/Bio/Tools/Run/Alignment/Amap.pm
  3. 1  lib/Bio/Tools/Run/Alignment/Clustalw.pm
  4. 1  lib/Bio/Tools/Run/Alignment/DBA.pm
  5. 1  lib/Bio/Tools/Run/Alignment/Exonerate.pm
  6. 1  lib/Bio/Tools/Run/Alignment/Gmap.pm
  7. 1  lib/Bio/Tools/Run/Alignment/Kalign.pm
  8. 1  lib/Bio/Tools/Run/Alignment/MAFFT.pm
  9. 1  lib/Bio/Tools/Run/Alignment/MSAProbs.pm
  10. 1  lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
  11. 1  lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
  12. 1  lib/Bio/Tools/Run/Alignment/TCoffee.pm
  13. 1  lib/Bio/Tools/Run/Analysis.pm
  14. 1  lib/Bio/Tools/Run/AnalysisFactory.pm
  15. 1  lib/Bio/Tools/Run/AssemblerBase.pm
  16. 1  lib/Bio/Tools/Run/BEDTools.pm
  17. 5  lib/Bio/Tools/Run/BWA.pm
  18. 1  lib/Bio/Tools/Run/BlastPlus.pm
  19. 1  lib/Bio/Tools/Run/Bowtie.pm
  20. 1  lib/Bio/Tools/Run/Cap3.pm
  21. 1  lib/Bio/Tools/Run/EMBOSSApplication.pm
  22. 1  lib/Bio/Tools/Run/EMBOSSacd.pm
  23. 1  lib/Bio/Tools/Run/ERPIN.pm
  24. 1  lib/Bio/Tools/Run/Ensembl.pm
  25. 1  lib/Bio/Tools/Run/Eponine.pm
  26. 1  lib/Bio/Tools/Run/FootPrinter.pm
  27. 1  lib/Bio/Tools/Run/Genemark.pm
  28. 1  lib/Bio/Tools/Run/Genewise.pm
  29. 1  lib/Bio/Tools/Run/Infernal.pm
  30. 1  lib/Bio/Tools/Run/MCS.pm
  31. 1  lib/Bio/Tools/Run/Maq.pm
  32. 1  lib/Bio/Tools/Run/Match.pm
  33. 1  lib/Bio/Tools/Run/Mdust.pm
  34. 1  lib/Bio/Tools/Run/Meme.pm
  35. 1  lib/Bio/Tools/Run/Phrap.pm
  36. 1  lib/Bio/Tools/Run/Primer3.pm
  37. 1  lib/Bio/Tools/Run/Profile.pm
  38. 1  lib/Bio/Tools/Run/Promoterwise.pm
  39. 1  lib/Bio/Tools/Run/RNAMotif.pm
  40. 1  lib/Bio/Tools/Run/RepeatMasker.pm
  41. 1  lib/Bio/Tools/Run/Samtools.pm
  42. 1  lib/Bio/Tools/Run/Samtools/Config.pm
  43. 1  lib/Bio/Tools/Run/Seg.pm
  44. 1  lib/Bio/Tools/Run/Simprot.pm
  45. 1  lib/Bio/Tools/Run/StandAloneBlastPlus.pm
1  lib/Bio/DB/ESoap.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::DB::ESoap
4 3
 #
1  lib/Bio/Tools/Run/Alignment/Amap.pm
... ...
@@ -1,3 +1,4 @@
  1
+#
1 2
 # BioPerl module for Bio::Tools::Run::Alignment::Amap
2 3
 #
3 4
 # Please direct questions and support issues to <bioperl-l@bioperl.org> 
1  lib/Bio/Tools/Run/Alignment/Clustalw.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::Alignment::Clustalw
4 3
 #
1  lib/Bio/Tools/Run/Alignment/DBA.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::Alignment::DBA
4 3
 #
1  lib/Bio/Tools/Run/Alignment/Exonerate.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # Please direct questions and support issues to <bioperl-l@bioperl.org>
4 3
 #
1  lib/Bio/Tools/Run/Alignment/Gmap.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::Alignment::Gmap
4 3
 #
1  lib/Bio/Tools/Run/Alignment/Kalign.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::Alignment::Kalign
4 3
 #
1  lib/Bio/Tools/Run/Alignment/MAFFT.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::Alignment::MAFFT
4 3
 #
1  lib/Bio/Tools/Run/Alignment/MSAProbs.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::Alignment::MSAProbs
4 3
 #
1  lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id: Pal2Nal.pm,v 1.3 2007/05/25 10:14:55 sendu Exp $
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::Alignment::Pal2Nal
4 3
 #
1  lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #StandAloneFasta.pm v1.00 2002/11/01 
3 2
 #
4 3
 #Bioperl module for Bio::Tools::Run::Alignment::StandAloneFasta
1  lib/Bio/Tools/Run/Alignment/TCoffee.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::Alignment::TCoffee
4 3
 #
1  lib/Bio/Tools/Run/Analysis.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::Analysis
4 3
 #
1  lib/Bio/Tools/Run/AnalysisFactory.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::AnalysisFactory
4 3
 #
1  lib/Bio/Tools/Run/AssemblerBase.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::AssemblerBase
4 3
 #
1  lib/Bio/Tools/Run/BEDTools.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id: BEDTools.pm kortsch $
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::BEDTools
4 3
 #
5  lib/Bio/Tools/Run/BWA.pm
... ...
@@ -1,6 +1,3 @@
1  
-# $Id$
2  
-package Bio::Tools::Run::BWA;
3  
-use strict;
4 1
 #
5 2
 # BioPerl module for Bio::Tools::Run::BWA
6 3
 #
@@ -171,6 +168,8 @@ Internal methods are usually preceded with a _
171 168
 
172 169
 # Let the code begin...
173 170
 
  171
+package Bio::Tools::Run::BWA;
  172
+use strict;
174 173
 
175 174
 use IPC::Run;
176 175
 our $HAVE_IO_UNCOMPRESS;
1  lib/Bio/Tools/Run/BlastPlus.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::BlastPlus
4 3
 #
1  lib/Bio/Tools/Run/Bowtie.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id: Bowtie.pm kortsch $
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::Bowtie
4 3
 #
1  lib/Bio/Tools/Run/Cap3.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 # You may distribute this module under the same terms as perl itself
3 2
 #
4 3
 # POD documentation - main docs before the code
1  lib/Bio/Tools/Run/EMBOSSApplication.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::EMBOSSApplication
4 3
 #
1  lib/Bio/Tools/Run/EMBOSSacd.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::EMBOSSacd
4 3
 #
1  lib/Bio/Tools/Run/ERPIN.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::ERPIN
4 3
 #
1  lib/Bio/Tools/Run/Ensembl.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id: Ensembl.pm,v 1.6 2006/07/17 14:16:53 sendu Exp $
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::Ensembl
4 3
 #
1  lib/Bio/Tools/Run/Eponine.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # Please direct questions and support issues to <bioperl-l@bioperl.org> 
4 3
 #
1  lib/Bio/Tools/Run/FootPrinter.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 # BioPerl module for FootPrinter
3 2
 #
4 3
 # Copyright Shawn Hoon
1  lib/Bio/Tools/Run/Genemark.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::Genemark
4 3
 #
1  lib/Bio/Tools/Run/Genewise.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # Please direct questions and support issues to <bioperl-l@bioperl.org> 
4 3
 #
1  lib/Bio/Tools/Run/Infernal.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # You may distribute this module under the same terms as perl itself
4 3
 #
1  lib/Bio/Tools/Run/MCS.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id: MCS.pm,v 1.3 2007/05/25 10:14:55 sendu Exp $
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::MCS
4 3
 #
1  lib/Bio/Tools/Run/Maq.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::Maq
4 3
 #
1  lib/Bio/Tools/Run/Match.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id: Match.pm,v 1.3 2007/05/25 10:14:55 sendu Exp $
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::Match
4 3
 #
1  lib/Bio/Tools/Run/Mdust.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Mdust
4 3
 #
1  lib/Bio/Tools/Run/Meme.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id: Meme.pm,v 1.25 2006/07/04 22:23:31 mauricio Exp $
2 1
 # BioPerl module for Meme
3 2
 #
4 3
 # Please direct questions and support issues to <bioperl-l@bioperl.org> 
1  lib/Bio/Tools/Run/Phrap.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # Phrap wraper module
4 3
 #
1  lib/Bio/Tools/Run/Primer3.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # This is the original copyright statement. I have relied on Chad's module
4 3
 # extensively for this module.
1  lib/Bio/Tools/Run/Profile.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 # BioPerl module for Profile
3 2
 # Copyright Balamurugan Kumarasamy
4 3
 #
1  lib/Bio/Tools/Run/Promoterwise.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id: Promoterwise.pm,
2 1
 #
3 2
 # Please direct questions and support issues to <bioperl-l@bioperl.org> 
4 3
 #
1  lib/Bio/Tools/Run/RNAMotif.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::RNAMotif
4 3
 #
1  lib/Bio/Tools/Run/RepeatMasker.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 # BioPerl module for RepeatMasker
3 2
 #
4 3
 # Please direct questions and support issues to <bioperl-l@bioperl.org>
1  lib/Bio/Tools/Run/Samtools.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::Samtools
4 3
 #
1  lib/Bio/Tools/Run/Samtools/Config.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::Samtools::Config
4 3
 #
1  lib/Bio/Tools/Run/Seg.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 # Copyright Balamurugan Kumarasamy
3 2
 # You may distribute this module under the same terms as perl itself
4 3
 #  POD documentation - main docs before the code
1  lib/Bio/Tools/Run/Simprot.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::Simprot
4 3
 #
1  lib/Bio/Tools/Run/StandAloneBlastPlus.pm
... ...
@@ -1,4 +1,3 @@
1  
-# $Id$
2 1
 #
3 2
 # BioPerl module for Bio::Tools::Run::StandAloneBlastPlus
4 3
 #

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