From: Bo Li <bli@cs.wisc.edu>
Date: Wed, 6 Jun 2012 02:02:46 +0000 (-0500)
Subject: Tested the codes
X-Git-Url: https://git.donarmstrong.com/?p=rsem.git;a=commitdiff_plain;h=6eec553ba4ab1cb1c6f48cd14d9e5c92c7d85798

Tested the codes
---

diff --git a/BamConverter.h b/BamConverter.h
index 13b8557..eaf2f66 100644
--- a/BamConverter.h
+++ b/BamConverter.h
@@ -101,7 +101,7 @@ void BamConverter::process() {
 
 
 		if (!notgood) {
-		  assert((b->core.tid == b2->core.tid) && (b->core.flag & 0x0040) && (b2->core.flag & 0x0080)); // for collapsing
+		  if (isPaired) assert((b->core.tid == b2->core.tid) && (b->core.flag & 0x0040) && (b2->core.flag & 0x0080)); // for collapsing
 
 		  const Transcript& transcript = transcripts.getTranscriptViaEid(b->core.tid + 1);
 
diff --git a/WHAT_IS_NEW b/WHAT_IS_NEW
index ddcfd95..3c7f654 100644
--- a/WHAT_IS_NEW
+++ b/WHAT_IS_NEW
@@ -1,3 +1,11 @@
+RSEM v1.1.20
+
+- Added an option to set the temporary folder name
+- Removed sample_name.sam.gz. Instead, RSEM uses samtools to convert bowtie outputed SAM file into a BAM file under the temporary folder
+- RSEM generated BAM files now contains all alignment lines produced by bowtie or user-specified aligners, including unalignable reads. Please note that for paired-end reads, if one mate has alignments but the other does not, RSEM will mark the alignable mate as "unmappable" (flag bit 0x4) and append an optional field "Z0:A:!"
+
+--------------------------------------------------------------------------------------------
+
 RSEM v1.1.19
 
 - Allowed > 2^31 hits
diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index 457f177..9e6ef2e 100755
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -310,7 +310,7 @@ if ($calcCI) {
     &collectResults("$imdName.iso_res", "$sampleName.isoforms.results"); # isoform level
     &collectResults("$imdName.gene_res", "$sampleName.genes.results"); # gene level
 
-    $command = $dir."rsem-calculate-credibility-intervals $refName $sampleName $sampleToken $CONFIDENCE $NCV $NSPC $NMB";
+    $command = $dir."rsem-calculate-credibility-intervals $refName $imdName $statName $CONFIDENCE $NCV $NSPC $NMB";
     $command .= " -p $nThreads";
     if ($quiet) { $command .= " -q"; }
     &runCommand($command);
@@ -482,7 +482,7 @@ Generate a BAM file, 'sample_name.genome.bam', with alignments mapped to genomic
 
 =item B<--sampling-for-bam>
 
-When RSEM generates a BAM file, instead of outputing all alignments a read has with their posterior probabilities, one alignment is sampled and outputed according to the posterior probabilities. If the sampling result is that the read comes from the "noise" transcript, nothing is outputed. (Default: off)
+When RSEM generates a BAM file, instead of outputing all alignments a read has with their posterior probabilities, one alignment is sampled according to the posterior probabilities. The sampling procedure includes the alignment to the "noise" transcript, which does not appear in the BAM file. Only the sampled alignment has a weight of 1. All other alignments have weight 0. If the "noise" transcript is sampled, all alignments appeared in the BAM file should have weight 0. (Default: off)
 
 =item B<--calc-ci>
 
@@ -646,7 +646,12 @@ is set to min(100, floor(-10 * log10(1.0 - w) + 0.5)), where w is the
 posterior probability of that alignment being the true mapping of a
 read.  In addition, RSEM pads a new tag ZW:f:value, where value is a
 single precision floating number representing the posterior
-probability.
+probability. Because this file contains all alignment lines produced
+by bowtie or user-specified aligners, it can also be used as a
+replacement of the aligner generated BAM/SAM file. For paired-end
+reads, if one mate has alignments but the other does not, this file
+marks the alignable mate as "unmappable" (flag bit 0x4) and appends an
+optional field "Z0:A:!".
 
 'sample_name.transcript.sorted.bam' and
 'sample_name.transcript.sorted.bam.bai' are the sorted BAM file and
@@ -671,12 +676,6 @@ indicating the strand of the transcript it aligns to.
 'sample_name.genome.sorted.bam' and 'sample_name.genome.sorted.bam.bai' are the
 sorted BAM file and indices generated by samtools (included in RSEM package).
 
-=item B<sample_name.sam.gz>
-
-Only generated when the input files are raw reads instead of SAM/BAM format files
-
-It is the gzipped SAM output produced by bowtie aligner.
-
 =item B<sample_name.time>
 
 Only generated when --time is specified.