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remove unused code

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commit afe19ebd2afa222a21f9f8fcc2dfa68d3bf683f1 1 parent 9941d69
@rmtheis authored
Showing with 0 additions and 64 deletions.
  1. +0 −64 IntronPoly.pm
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64 IntronPoly.pm
@@ -375,53 +375,6 @@ sub bowtie2_identify {
$ofh3->close;
}
-# =head2 find_distant_alignments
-#
-# Title : find_distant_alignments
-# Usage :
-# Function: Run Bowtie to find read pairs where both mates align concordantly, but far from one another
-# Example :
-# Returns :
-# Args :
-#
-# =cut
-#
-# sub find_distant_alignments {
-# my $self = shift;
-# my $num_threads = shift;
-# my $data_basename = $self->{"data_basename"};
-# my $ref_genome_basename = $self->{"ref_genome"}->{"basename"};
-# my $bowtie2_dir = $self->{"bowtie_db"}->{"bowtie2_dir"};
-# my $bowtie_index_dir = $self->{"bowtie_db"}->{"bowtie_index_dir"};
-# my $reads_file_one = $self->{"bowtie_db"}->{"reads_file_one"};
-# my $reads_file_two = $self->{"bowtie_db"}->{"reads_file_two"};
-# my $work_dir = $self->{"work_dir"};
-# print "Running mapping using bowtie2 to find distant alignments, using $num_threads threads...\n";
-#
-# # Combine the read pairs files into one file with unique IDs for unpaired mapping
-# my $unpaired_reads_file = "$work_dir/${data_basename}_unpaired.fq";
-# &_combine_fastq( $reads_file_one, $reads_file_two, $unpaired_reads_file );
-#
-#
-# # Call bowtie to run the mapping as unpaired reads
-# my $results = capture( "$bowtie2_dir/bowtie2 -x $bowtie_index_dir/$ref_genome_basename " .
-# "--threads $num_threads --reorder --sam-no-hd " .
-# "--no-discordant --no-contain --no-overlap " .
-# "-k 3 -U $reads_file_one,$reads_file_two " .
-# #"--al-conc $work_dir/${data_basename}_al-conc.%.fq " .
-# #"--un-conc $work_dir/${data_basename}_un-conc.%.fq " .
-# "-S $work_dir/${data_basename}_halfmapping3.sam.tmp"
-# );
-#
-# if( $EXITVAL != 0 ) {
-# die "$0: bowtie2 exited unsuccessful";
-# }
-#
-# # Parse the alignments file to compare distances between reads
-#
-# print "debug: find_distant_alignments() done.\n";
-# }
-
=head2 filter
Title : filter
@@ -782,23 +735,6 @@ sub _isUnalignedMate {
}
}
-# Combines two FastQ files, appending "-1" and "-2" to the read IDs for uniqueness
-sub _combine_fastq {
- my $input_file1 = shift;
- my $input_file2 = shift;
- my $output_file = shift;
- my $ifh1 = new IO::File($input_file1, 'r') or die "$0: Can't open $input_file1: $!";
- my $ifh2 = new IO::File($input_file2, 'r') or die "$0: Can't open $input_file2: $!";
- my $ofh = new IO::File($output_file, 'w') or die "$0: Can't open $output_file: $!";
-
- while ( my $line = $ifh1->getline ) {
- print $ofh $line; #TODO change the IDs. Put "-1" before any "/1"
- }
- while ( my $line = $ifh2->getline ) {
- print $ofh $line; #TODO change the IDs.
- }
-}
-
# Checks if the given folder exists, and removes trailing slash from string
sub _check_dir {
my $dir = shift;
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