For genome BAM, modified MD tag accordingly

[rsem.git] / WHAT_IS_NEW

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+RSEM v1.2.13
+
+- Allowed users to use the SAMtools in the PATH first and enabled RSEM to find its executables via a symbolic link
+- Changed the behavior of parsing GTF file. Now if a GTF line's feature is not "exon" and it does not contain a "gene_id" or "transcript_id" attribute, only a warning message will be produced (instead of failing the RSEM)
+
+--------------------------------------------------------------------------------------------
+
+RSEM v1.2.12
+
+- Enabled allele-specific expression estimation
+- Added '--calc-pme' option for 'rsem-calculate-expression' to calculate posterior mean estimates only (no credibility intervals)
+- Modified the shebang line of RSEM perl scripts to make them more portable
+- Added '--seed' option for 'rsem-simulate-reads' to enable users set the seed of random number generator used by the simulation
+- Modified the transcript extraction behavior of 'rsem-prepare-reference'. For transcripts that cannot be extracted, instead of failing the whole script, warning information is produced. Those transcripts are ignored
+
+--------------------------------------------------------------------------------------------
+
 RSEM v1.2.11
 
 - Enabled RSEM to use Bowtie 2 aligner (indel, local and discordant alignments are not supported yet)