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Upgraded SAMtools to v1.3; RSEM now supports input alignments in SAM/BAM/CRAM format
'--sam/--bam' options of 'rsem-calculate-expression' are obsoleted; use '--alignments' instead; '--sam/--bam' can still be used for compatibility with previous versions
Some 'rsem-calculate-expression' options are renamed for better interpretability
Documents are updated to reflect the SAMtools upgrade
Fixed a bug for parsing GTF files
Fixed a bug for generating transcript wiggle plots
