updated files to do release

CHANGES.md

@@ -1,5 +1,10 @@
 # Changes
 
+## 4.4.0
+
+* Added ascatCounts to produce counts files
+* Modified ascat wrapper to handle count files as input
+
 ## 4.3.4
 
 * Eliminated redundant logic from setup script

perl/MANIFEST

@@ -1,5 +1,6 @@
 bin/ascat.pl
 bin/ascatCnToVCF.pl
+bin/ascatCounts.pl
 bin/ascatFailedCnCsv.pl
 bin/ascatToBigWig.pl
 bin/utilities/ascatFaiChunk.pl
@@ -21,23 +22,24 @@ docs/pod_html/_whtprpk.css
 docs/pod_html/_whtpurk.css
 docs/pod_html/ascat.html
 docs/pod_html/ascatCnToVCF.html
+docs/pod_html/ascatCounts.html
 docs/pod_html/ascatFailedCnCsv.html
 docs/pod_html/ascatToBigWig.html
 docs/pod_html/index.html
 docs/pod_html/Sanger/CGP/Ascat.html
 docs/pod_html/utilities/ascatSnpPanelGenerator.html
-docs/reports_html/blib-lib-Sanger-CGP-Ascat-Implement-pm--branch.html
-docs/reports_html/blib-lib-Sanger-CGP-Ascat-Implement-pm--subroutine.html
-docs/reports_html/blib-lib-Sanger-CGP-Ascat-Implement-pm.html
-docs/reports_html/blib-lib-Sanger-CGP-Ascat-pm--subroutine.html
-docs/reports_html/blib-lib-Sanger-CGP-Ascat-pm.html
 docs/reports_html/common.js
 docs/reports_html/cover.14
 docs/reports_html/cover.css
 docs/reports_html/coverage.html
 docs/reports_html/css.js
 docs/reports_html/digests
 docs/reports_html/index.html
+docs/reports_html/lib-Sanger-CGP-Ascat-Implement-pm--branch.html
+docs/reports_html/lib-Sanger-CGP-Ascat-Implement-pm--subroutine.html
+docs/reports_html/lib-Sanger-CGP-Ascat-Implement-pm.html
+docs/reports_html/lib-Sanger-CGP-Ascat-pm--subroutine.html
+docs/reports_html/lib-Sanger-CGP-Ascat-pm.html
 docs/reports_html/standardista-table-sorting.js
 docs/reports_text/coverage.txt
 lib/Sanger/CGP/Ascat.pm

perl/lib/Sanger/CGP/Ascat.pm

@@ -26,7 +26,7 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '4.3.4';
+our $VERSION = '4.4.0';
 our @EXPORT = qw($VERSION);
 
 const my $LICENSE =>