/usr/bin/convert-sam-for-rsem is in rsem 1.2.31+dfsg-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 | #!/usr/bin/env perl
use Getopt::Long;
use Pod::Usage;
use File::Basename;
use FindBin;
use lib $FindBin::RealBin;
use rsem_perl_utils qw(runCommand getSAMTOOLS);
use Env qw(@PATH);
@PATH = ($FindBin::RealBin, "$FindBin::RealBin/" . getSAMTOOLS(), @PATH);
use strict;
my $p = 1;
my $mem = "1G";
my $help = 0;
GetOptions("p|num-threads=i" => \$p,
"memory-per-thread=s" => \$mem,
"h|help" => \$help) or pd2usage(-exitval => 2, -verbose => 2);
pod2usage(-verbose => 2) if ($help == 1);
pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2) if (scalar(@ARGV) != 2);
my $command;
my $in_file = $ARGV[0];
my $tmp_file = "$ARGV[1].tmp.bam";
my $out_file = "$ARGV[1].bam";
# Phase I, sort entries so that all entries of a same read groups together
$command = "samtools sort -n -@ $p -m $mem -o $tmp_file $in_file";
&runCommand($command);
# Phase II, parse the temporary BAM file to make paired-end alignments' two mates adjacent to each other
$command = "rsem-scan-for-paired-end-reads $p $tmp_file $out_file";
&runCommand($command);
# delete temporary file
unlink $tmp_file or die "Could not delete $tmp_file.";
print "Conversion is completed. $out_file will be checked by 'rsem-sam-validator'.\n";
# Phase III, validate if the resulting bam file is correct
$command = "rsem-sam-validator $out_file";
&runCommand($command);
__END__
=head1 NAME
convert-sam-for-rsem
=head1 PURPOSE
Make a RSEM compatible BAM file.
=head1 SYNOPSIS
convert-sam-for-rsem [options] <input.sam/input.bam/input.cram> output_file_name
=head1 ARGUMENTS
=over
=item B<input.sam/input.bam/input.cram>
The SAM/BAM/CRAM file generated by user's aligner. We require this file contains the header section.
=item B<output_file_name>
The output name for the converted file. 'convert-sam-for-rsem' will output a BAM with the name 'output_file_name.bam'.
=back
=head1 OPTIONS
=over
=item B<-p/--num-threads> <int>
Set the number of threads to be used for converting. (Default: 1)
=item B<--memory-per-thread> <string>
Set the maximum allowable memory per thread. <string> represents the memory and accepts suffices 'K/M/G'. (Default: 1G)
=item B<-h/--help>
Show help information.
=back
=head1 DESCRIPTION
This program converts the SAM/BAM/CRAM file generated by user's aligner into a BAM file which RSEM can process. However, users should make sure their aligners use 'reference_name.idx.fa' generated by 'rsem-prepare-reference' as their references and output header sections. After the conversion, this program will call 'rsem-sam-validator' to validate the resulting BAM file.
Note: You do not need to run this script if `rsem-sam-validator' reports that your SAM/BAM/CRAM file is valid.
=head1 EXAMPLES
Suppose input is set to 'input.sam' and output file name is "output"
convert-sam-for-rsem input.sam output
We will get a file called 'output.bam' as output.
=cut
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