add --no-bam-output option to not generate output bam files

diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index 00f26cee381fdf03f6028748bda1caa1aa9190ae..5614ecda945f8fe2b261fff8e3c9ed5bc891979d 100755 (executable)
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -86,6 +86,7 @@ GetOptions("keep-intermediate-files" => \$keep_intermediate_files,
           "estimate-rspd" => \$estRSPD,
           "num-rspd-bins=i" => \$B,
           "p|num-threads=i" => \$nThreads,
+          "no-bam-output" => sub { $genBamF = 0; },
           "output-genome-bam" => \$genGenomeBamF,
           "sampling-for-bam" => \$sampling,
           "calc-ci" => \$calcCI,
@@ -116,7 +117,8 @@ pod2usage(-msg => "Min fragment length should be smaller or equal to max fragmen
 pod2usage(-msg => "The memory allocated for calculating credibility intervals should be at least 1 MB!\n", -exitval => 2, -verbose => 2) if ($NMB < 1);
 pod2usage(-msg => "Number of threads should be at least 1!\n", -exitval => 2, -verbose => 2) if ($nThreads < 1);
 pod2usage(-msg => "Seed length should be at least 5!\n", -exitval => 2, -verbose => 2) if ($L < 5);
-pod2usage(-msg => "--sampling-for-bam cannot be specified if --out-bam is not specified!\n", -exitval => 2, -verbose => 2) if ($sampling && !$genBamF);
+pod2usage(-msg => "--sampling-for-bam cannot be specified if --no-bam-output is specified!\n", -exitval => 2, -verbose => 2) if ($sampling && !$genBamF);
+pod2usage(-msg => "--output-genome-bam cannot be specified if --no-bam-output is specified!\n", -exitval => 2, -verbose => 2) if ($genGenomeBamF && !$genBamF);
 
 if ($L < 25) { print "Warning: the seed length set is less than 25! This is only allowed if the references are not added poly(A) tails.\n"; }
 
@@ -463,6 +465,10 @@ RSEM reads header information from input by default. If this option is on, heade
 
 Number of threads to use. Both Bowtie and expression estimation will use this many threads. (Default: 1)
 
+=item B<--no-bam-output>
+
+Do not output any BAM file. (Default: off)
+
 =item B<--output-genome-bam>
 
 Generate a BAM file, 'sample_name.genome.bam', with alignments mapped to genomic coordinates and annotated with their posterior probabilities. In addition, RSEM will call samtools (included in RSEM package) to sort and index the bam file. 'sample_name.genome.sorted.bam' and 'sample_name.genome.sorted.bam.bai' will be generated. (Default: off)
@@ -621,6 +627,8 @@ provided, 'gene_id' and 'transcript_id' are the same.
 
 =item B<sample_name.transcript.bam, sample_name.transcript.sorted.bam and sample_name.transcript.sorted.bam.bai>
 
+Only generated when --no-bam-output is not specified.
+
 'sample_name.transcript.bam' is a BAM-formatted file of read
 alignments in transcript coordinates. The MAPQ field of each alignment
 is set to min(100, floor(-10 * log10(1.0 - w) + 0.5)), where w is the
@@ -635,7 +643,7 @@ indices generated by samtools (included in RSEM package).
 
 =item B<sample_name.genome.bam, sample_name.genome.sorted.bam and sample_name.genome.sorted.bam.bai>
 
-Only generated when --output-genome-bam is specified.
+Only generated when --no-bam-output is not specified and --output-genome-bam is specified.
 
 'sample_name.genome.bam' is a BAM-formatted file of read alignments in
 genomic coordinates. Alignments of reads that have identical genomic