3 - Fixed a bug related to parallezation of credibility intervals calculation
4 - Added --no-bam-output option to rsem-calculate-expression
5 - The order of @SQ tags in SAM/BAM files can be arbitrary now
7 --------------------------------------------------------------------------------------------
11 - Added --time option to show time consumed by each phase
12 - Moved the alignment file out of the temporary folder
13 - Enabled pthreads for calculating credibility intervals
15 --------------------------------------------------------------------------------------------
19 - Fixed several bugs causing compilation error
20 - Modified samtools' Makefile for cygwin. For cygwin users, please uncomment the 4th and 8th lines in sam/Makefile before compiling RSEM
22 --------------------------------------------------------------------------------------------
26 - Added --chunkmbs option to rsem-calculate-expression (patch contributed by earonesty)
27 - Added --sampling-for-bam option to rsem-calculate-expression, in the bam file, instead of providing expected weights, for each read RSEM samples one alignment based on the expected weights
28 - RSEM can generate BAM and Wiggle files in both genomic-coordinate and transcript-coordinate
29 - Added rsem-plot-transcript-wiggles. This script can generate transcript-coordinate wiggle plots in pdf format. One unique feature is, a stacked plot can be generated, with unique read contribution shown as black and multi-read contribution shown as red
30 - Added convert_sam_for_rsem script for users do not use bowtie aligner
31 - Modified RSEM's GTF file parser. Now RSEM does not require "transcript_id" and "gene_id" be the first two attributes shown
32 - Improved descriptions for thread related errors