RSEM v1.3.0

• Added Prior-Enhanced RSEM (pRSEM) as a submodule
• Introduced --strandedness <none|forward|reverse> option, --strand-specific and --forward-prob are deprecated (but still supported)
• Revised documentation for rsem-plot-model, maked it clear that in alignment statistics, isoform-level (instead of genome-level) multi-mapping reads are shown
• Significantly improved the output information of rsem-sam-validator: if indels/clippings/skips are detected in alignments or alignments exceed transcript boundaries, rsem-sam-validator will report them instead of telling you the input is valid
• Updated the warning message to ask users to make sure that they align their reads agains a set of transcripts instead of genome when RSEM finds less sequences in the BAM file than RSEM's indices