Merge branch 'hotfix/v3.3.1'

* Fixed bug when creating split loci files which would occasionally count wrongly due to rounding errors. Fixed the cause of the rounding error and added a sort to the hash.
* Added check that the number of split loci files is at least the number of required contigs

.travis.yml

@@ -20,6 +20,8 @@ addons:
     - time
     - curl
     - r-base-dev
+    - libgd-dev
+    - libdb-dev
 
 install: true
 

CHANGES.md

@@ -1,5 +1,11 @@
 # Changes
 
+## 3.3.1
+
+* Fixed bug when creating split loci files which would occasionally count wrongly due to rounding errors. Fixed the cause of the rounding error and added a sort to the hash.
+* Added check that the number of split loci files is at least the number of required contigs
+
+
 ## 3.3.0
 
 * Upgrade to Battenberg [v2.2.8](https://github.com/Wedge-Oxford/battenberg/releases/tag/v2.2.8).

perl/bin/battenberg.pl

@@ -292,6 +292,9 @@ sub setup {
     $opts{'num_loci_files'} = $no_of_jobs;
     $loci_files_defined = 0;
   }
+  if ($opts{'num_loci_files'} < $no_of_jobs) {
+    die "ERROR: Please define at least as many loci files (" . $opts{'num_loci_files'} . ") as required contigs ($no_of_jobs)";
+  }
 
 	if(exists $opts{'process'}) {
     PCAP::Cli::valid_process('process', $opts{'process'}, \@VALID_PROCESS);

perl/lib/Sanger/CGP/Battenberg.pm

@@ -25,7 +25,7 @@ use strict;
 
 use Const::Fast qw(const);
 use base 'Exporter';
-our $VERSION = '3.3.0';
+our $VERSION = '3.3.1';
 our @EXPORT = qw($VERSION);
 
 1;

perl/lib/Sanger/CGP/Battenberg/Implement.pm

@@ -239,29 +239,29 @@ sub battenberg_splitlocifiles {
   my $num_loci_per_split = $total_loci_remaining / $num_loci_files;
 
   my $total_number_of_split_files_created = 0;
-
-  foreach my $file (keys %$loci_per_file) {
+  foreach my $file (sort keys %$loci_per_file) {
 
     #Check if we are at the last file
     my $number_of_split_files_for_chr;
     if ($total_loci_remaining == $loci_per_file->{$file}) {
       #Set last file to be what is left
       $number_of_split_files_for_chr = $requested_num_loci_files - $total_number_of_split_files_created;
     } else {
-      $number_of_split_files_for_chr = int($loci_per_file->{$file} / $num_loci_per_split);
+      $number_of_split_files_for_chr = $loci_per_file->{$file} / $num_loci_per_split;
     }
 
     #Must have each file at least once
-    if ($number_of_split_files_for_chr == 0) {
-      $number_of_split_files_for_chr = 1;
-    }
     #print "file=$file " . $loci_per_file->{$file} . " $number_of_split_files_for_chr $total_number_of_split_files_created\n";
+    my $int_number_of_split_files_for_chr = int($number_of_split_files_for_chr);
+    if ($int_number_of_split_files_for_chr < 1) {
+      $int_number_of_split_files_for_chr = 1;
+    }
 
     #Write split loci files to the tmpdir
-    _create_split_files($file, $loci_per_file->{$file}, $number_of_split_files_for_chr, $tmp, $total_number_of_split_files_created);
+    _create_split_files($file, $loci_per_file->{$file}, $int_number_of_split_files_for_chr, $tmp, $total_number_of_split_files_created);
 
     #Keep track of the total number of files created
-    $total_number_of_split_files_created += $number_of_split_files_for_chr;
+    $total_number_of_split_files_created += $int_number_of_split_files_for_chr;
 
     #Need to keep refining the answer to avoid problems with rounding
     if ($num_loci_files > $number_of_split_files_for_chr) {
@@ -270,7 +270,7 @@ sub battenberg_splitlocifiles {
   }
 
   if ($total_number_of_split_files_created != $requested_num_loci_files) {
-    die("The number of loci files created $total_number_of_split_files_created is not the same as the number requested $num_loci_files\n");
+    die("The number of loci files created $total_number_of_split_files_created is not the same as the number requested $requested_num_loci_files\n");
   }
   return PCAP::Threaded::touch_success(File::Spec->catdir($tmp, 'progress'), 0);
 }