Merge branch 'release/v3.3.0'

cancerit · Mar 7, 2018 · b0b5c20 · b0b5c20
2 parents b0def12 + 5f38092
commit b0b5c20
Show file tree

Hide file tree

Showing 11 changed files with 1,196 additions and 739 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,3 +1,6 @@
+### 3.3.0
+* Complete re-write of the reference generation code
+
 ### 3.2.2
 * Add bedtools2 to `setup.sh`
 * Added bedtools2 to `README.md`

diff --git a/MANIFEST b/MANIFEST
@@ -1,7 +1,7 @@
 .travis.yml
-bin/Admin_EnsemblGtf2CacheConverter.pl
+bin/Admin_CacheFileBuilder.pl
 bin/Admin_EnsemblReferenceFileGenerator.pl
-bin/Admin_EnsemblTranscriptFastaFilter.pl
+bin/Admin_EnsemblTranscriptFilter.pl
 bin/Admin_GeneRegionBedDumper.pl
 bin/AnnotateVcf.pl
 bin/cpanm

diff --git a/Makefile.PL b/Makefile.PL
@@ -31,9 +31,9 @@ WriteMakefile(
   NAME          => 'Vagrent',
   LICENSE       => 'agpl_3', # http://search.cpan.org/~dagolden/CPAN-Meta-2.142690/lib/CPAN/Meta/Spec.pm#license
   VERSION_FROM  => 'lib/Sanger/CGP/Vagrent.pm',
-  EXE_FILES     => [qw( bin/Admin_EnsemblGtf2CacheConverter.pl
+  EXE_FILES     => [qw( bin/Admin_CacheFileBuilder.pl
                         bin/Admin_EnsemblReferenceFileGenerator.pl
-                        bin/Admin_EnsemblTranscriptFastaFilter.pl
+                        bin/Admin_EnsemblTranscriptFilter.pl
                         bin/Admin_GeneRegionBedDumper.pl
                         bin/AnnotateVcf.pl)],
   PREREQ_PM     => {

diff --git a/README.md b/README.md
@@ -49,9 +49,9 @@ Please be aware that this expects basic C compilation libraries and tools to be
 LICENCE
 =======
 
-Copyright (c) 2014-2017 Genome Research Ltd.
+Copyright (c) 2014-2018 Genome Research Ltd.
 
-Author: Cancer Genome Project <cgpit@sanger.ac.uk>
+Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>
 
 This file is part of VAGrENT.