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keiranmrainekeiranmraine
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Merge branch 'hotfix/v6.0.1'
2 parents e5ba348 + 4d1a75f commit 128caf0

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13 files changed

+25
-25
lines changed

13 files changed

+25
-25
lines changed

‎perl/MANIFEST‎

Lines changed: 0 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -51,7 +51,6 @@ lib/Sanger/CGP/Rearrangement/Path.pm
5151
Makefile.PL
5252
MANIFEST This list of files
5353
MANIFEST.SKIP
54-
perltidy.LOG
5554
share/Rdefaults/Human.GRCh37.CentTelo.tsv
5655
share/Rscripts/.Rhistory
5756
share/Rscripts/filter_small_deletions_and_fb_artefacts.R

‎perl/bin/brass-assemble‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -380,7 +380,7 @@ sub assemble {
380380

381381
foreach my $cat (sort {$a <=> $b} keys %contrib_read_names){
382382
$contrib_read_string .= q{|} if($contrib_read_string);
383-
$contrib_read_string .= join(q{,}, @{$contrib_read_names{$cat}});
383+
$contrib_read_string .= join(q{,}, sort @{$contrib_read_names{$cat}});
384384
}
385385

386386
if (defined $bedpe) {

‎perl/bin/brass.pl‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -193,7 +193,7 @@ sub cleanup {
193193
my $intermediates_dir = File::Spec->catdir($outdir, 'intermediates');
194194
my $targz = $basefile.'.intermediates.tar.gz';
195195
unless(-e $targz && -s $targz) {
196-
system(qq{tar zcf $targz $intermediates_dir}) and die $!;
196+
system(qq{tar -C $outdir -zcf $targz $intermediates_dir}) and die $!;
197197
}
198198

199199
my $tmplogs = File::Spec->catdir($tmpdir, 'logs');

‎perl/bin/filter_with_microbes_and_remapping.pl‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -449,7 +449,7 @@ sub get_remapping_score_differences {
449449
unlink $source_fh_name or warn $!;
450450

451451
my @diffs;
452-
for(keys %{$source_scores}) {
452+
for(sort keys %{$source_scores}) {
453453
$target_scores->{$_} ||= 0;
454454
push @diffs, $source_scores->{$_} - $target_scores->{$_};
455455
}

‎perl/bin/get_abs_bkpts_from_clipped_reads.pl‎

Lines changed: 7 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -526,8 +526,9 @@
526526
else {
527527
$low_end_low_clip = ($low_end_low_clip_count >= $CLIPPED_READS_NEEDED ? "$low_end_low_clip_pos ($low_end_low_clip_count)" : lowest_pos_of_reads($low_end_reads_of_rg{$F[6]}) . ' (0)');
528528
$low_end_high_clip = ($low_end_high_clip_count >= $CLIPPED_READS_NEEDED ? "$low_end_high_clip_pos ($low_end_high_clip_count)" : highest_pos_of_reads($low_end_reads_of_rg{$F[6]}) . ' (0)');
529-
$low_end_read_uniq = join(',', unique(map { $_->query->name } @{$low_end_reads_of_rg{$F[6]}}));
530-
$low_end_read_count = scalar(unique(@{$low_end_reads_of_rg{$F[6]}}));
529+
my @tmpReads = unique(map { $_->query->name } @{$low_end_reads_of_rg{$F[6]}});
530+
$low_end_read_uniq = join(',', @tmpReads);
531+
$low_end_read_count = scalar(@tmpReads);
531532
}
532533

533534
if(exists $no_end_reads{$F[6]}{'high'}) {
@@ -540,8 +541,9 @@
540541
else {
541542
$high_end_low_clip = ($high_end_low_clip_count >= $CLIPPED_READS_NEEDED ? "$high_end_low_clip_pos ($high_end_low_clip_count)" : lowest_pos_of_reads($high_end_reads_of_rg{$F[6]}) . ' (0)');
542543
$high_end_high_clip = ($high_end_high_clip_count >= $CLIPPED_READS_NEEDED ? "$high_end_high_clip_pos ($high_end_high_clip_count)" : highest_pos_of_reads($high_end_reads_of_rg{$F[6]}) . ' (0)');
543-
$high_end_read_uniq = join(',', unique(map { $_->query->name } @{$high_end_reads_of_rg{$F[6]}}));
544-
$high_end_read_count = scalar(unique(@{$high_end_reads_of_rg{$F[6]}}));
544+
my @tmpReads = unique(map { $_->query->name } @{$high_end_reads_of_rg{$F[6]}});
545+
$high_end_read_uniq = join(',', @tmpReads);
546+
$high_end_read_count = scalar(@tmpReads);
545547
}
546548

547549
print $outfh join(
@@ -676,5 +678,5 @@ sub unique {
676678
for (@_) {
677679
$seen{$_} = 1;
678680
}
679-
return keys %seen;
681+
return sort {$a cmp $b} keys %seen;
680682
}

‎perl/bin/merge_double_rgs.pl‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -74,7 +74,7 @@
7474
}
7575

7676
my %to_be_excluded;
77-
for my $id (keys %id_overlaps_with) {
77+
for my $id (sort {$a <=> $b} keys %id_overlaps_with) {
7878
for (@{$id_overlaps_with{$id}}) {
7979
if ($data_of_id{$id}->[7] < $_->[1] || ($data_of_id{$id}->[7] == $_->[1] && $id gt $_->[0])) {
8080
$to_be_excluded{$id} = 1;
@@ -114,4 +114,3 @@
114114
close $IN;
115115

116116
close $fh if(@ARGV == 2);
117-

‎perl/docs.tar.gz‎

14.4 KB
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‎perl/lib/Bio/Brass.pm‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -46,7 +46,7 @@ our @EXPORT = qw(find_breakpoints find_dusty_vertices
4646
is_dusty get_isolated_bp_alignment get_isolated_bp_surrounding_region
4747
$VERSION);
4848

49-
our $VERSION = '6.0.0';
49+
our $VERSION = '6.0.1';
5050

5151
=head1 NAME
5252

‎perl/lib/Bio/Brass/ReadSelection.pm‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -284,7 +284,7 @@ sub write_local_reads {
284284
return (0,$k2+$d2) if($k2 >= $abort_reads); # artificially block extreme depth from assembly
285285

286286
my $k_count = 0;
287-
for my $pair(keys %{$k_reads}) {
287+
for my $pair(sort keys %{$k_reads}) {
288288
# unmapped mates which had a poor quality mapping
289289
# are discarded by this section
290290
next if(first { $_ eq $pair } @{$q_pairs});

‎perl/lib/Sanger/CGP/BrassFilter/BlatFlag.pm‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -306,7 +306,7 @@ sub _get_hits {
306306
# load an indexed fasta file
307307
my $fai = Bio::DB::HTS::Fai->load( $self->{ref} );
308308

309-
foreach my $name(keys %{$self->{data}}) {
309+
foreach my $name(sort keys %{$self->{data}}) {
310310
my $Lrange = $self->{data}->{$name}->{Lrange};
311311
my $Hrange = $self->{data}->{$name}->{Hrange};
312312

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