Updated samtools to 0.1.19

[rsem.git] / rsem-calculate-expression

diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index 4fbb4a59beac6a449a90e4dc6335d7a9633f6dcc..3f2817d083fac4605cbcb0ded7baaa6e6900db99 100755 (executable)
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -2,7 +2,8 @@
 
 use Getopt::Long;
 use Pod::Usage;
-use File::Basename;
+use FindBin;
+use lib $FindBin::Bin;
 use strict;
 
 use rsem_perl_utils qw(runCommand collectResults showVersionInfo);
@@ -87,9 +88,9 @@ GetOptions("keep-intermediate-files" => \$keep_intermediate_files,
           "bowtie-e=i" => \$E,
           "bowtie-m=i" => \$maxHits,
           "bowtie-chunkmbs=i" => \$chunkMbs,
-          "phred33-quals" => \$phred33,
-          "phred64-quals" => \$phred64, #solexa1.3-quals" => \$phred64,
-          "solexa-quals" => \$solexa,
+          "bowtie-phred33-quals" => \$phred33,
+          "bowtie-phred64-quals" => \$phred64, #solexa1.3-quals" => \$phred64,
+          "bowtie-solexa-quals" => \$solexa,
           "forward-prob=f" => \$probF,
           "fragment-length-min=i" => \$minL,
           "fragment-length-max=i" => \$maxL,
@@ -109,7 +110,7 @@ GetOptions("keep-intermediate-files" => \$keep_intermediate_files,
           "q|quiet" => \$quiet,
           "h|help" => \$help) or pod2usage(-exitval => 2, -verbose => 2);
 
-my ($fn, $dir, $suf) = fileparse($0);
+my $dir = "$FindBin::Bin/";
 
 pod2usage(-verbose => 2) if ($help == 1);
 &showVersionInfo($dir) if ($version == 1);
@@ -353,14 +354,10 @@ rsem-calculate-expression
 
 =head1 SYNOPSIS
 
-=over
-
- rsem-calculate-expression [options] upstream_read_file(s) reference_name sample_name
- rsem-calculate-expression [options] --paired-end upstream_read_file(s) downstream_read_file(s) reference_name sample_name
+ rsem-calculate-expression [options] upstream_read_file(s) reference_name sample_name 
+ rsem-calculate-expression [options] --paired-end upstream_read_file(s) downstream_read_file(s) reference_name sample_name 
  rsem-calculate-expression [options] --sam/--bam [--paired-end] input reference_name sample_name
 
-=back
-
 =head1 ARGUMENTS
 
 =over
@@ -463,17 +460,17 @@ The path to the bowtie executables. (Default: the path to the bowtie executables
 
 (Bowtie parameter) memory allocated for best first alignment calculation (Default: 0 - use bowtie's default)
 
-=item B<--phred33-quals>
+=item B<--bowtie-phred33-quals>
 
-Input quality scores are encoded as Phred+33. (Default: on)
+(Bowtie parameter) Input quality scores are encoded as Phred+33. (Default: on)
 
-=item B<--phred64-quals>
+=item B<--bowtie-phred64-quals>
 
-Input quality scores are encoded as Phred+64 (default for GA Pipeline ver. >= 1.3). (Default: off)
+(Bowtie parameter) Input quality scores are encoded as Phred+64 (default for GA Pipeline ver. >= 1.3). (Default: off)
 
-=item B<--solexa-quals>
+=item B<--bowtie-solexa-quals>
 
-Input quality scores are solexa encoded (from GA Pipeline ver. < 1.3). (Default: off)
+(Bowtie parameter) Input quality scores are solexa encoded (from GA Pipeline ver. < 1.3). (Default: off)
 
 =item B<--forward-prob> <double>
 
@@ -527,6 +524,10 @@ Suppress the output of logging information. (Default: off)
 
 Show help information.
 
+=item B<--version>
+
+Show version information.
+
 =back
 
 =head1 DESCRIPTION
@@ -717,7 +718,7 @@ Assume the path to the bowtie executables is in the user's PATH environment vari
                            /ref/mouse_125 \
                            mmliver_single_without_quals
 
-4) Data are the same as 1). We want to take a fragment length distribution into consideration. We set the fragment length mean to 150 and the standard deviation to 35. In addition to a BAM file, we also want to generate credibility intervals.  We allow RSEM to use 1GB of memory for CI calculation:
+4) Data are the same as 1). This time we assume the bowtie executables are under '/sw/bowtie'. We want to take a fragment length distribution into consideration. We set the fragment length mean to 150 and the standard deviation to 35. In addition to a BAM file, we also want to generate credibility intervals.  We allow RSEM to use 1GB of memory for CI calculation:
 
  rsem-calculate-expression --bowtie-path /sw/bowtie \
                            --phred64-quals \