From cb94fd597b180aa7cb01ae84c9d1025201b98d8e Mon Sep 17 00:00:00 2001 From: Bo Li Date: Wed, 8 Feb 2012 10:38:25 -0600 Subject: [PATCH] add --no-bam-output option to not generate output bam files --- rsem-calculate-expression | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/rsem-calculate-expression b/rsem-calculate-expression index 00f26ce..5614ecd 100755 --- 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 +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 -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 -- 2.39.2