3 - Added some user-friendly error messages
4 - Added program 'rsem-sam-validator', users can use this program to check if RSEM can process their SAM/BAM files
5 - Modified 'convert-sam-for-rsem' so that this program will convert users' SAM/BAM files into acceptable BAM files for RSEM
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11 - Fixed a bug related to parallezation of credibility intervals calculation
12 - Added --no-bam-output option to rsem-calculate-expression
13 - The order of @SQ tags in SAM/BAM files can be arbitrary now
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19 - Added --time option to show time consumed by each phase
20 - Moved the alignment file out of the temporary folder
21 - Enabled pthreads for calculating credibility intervals
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27 - Fixed several bugs causing compilation error
28 - Modified samtools' Makefile for cygwin. For cygwin users, please uncomment the 4th and 8th lines in sam/Makefile before compiling RSEM
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34 - Added --chunkmbs option to rsem-calculate-expression (patch contributed by earonesty)
35 - 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
36 - RSEM can generate BAM and Wiggle files in both genomic-coordinate and transcript-coordinate
37 - 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
38 - Added convert_sam_for_rsem script for users do not use bowtie aligner
39 - Modified RSEM's GTF file parser. Now RSEM does not require "transcript_id" and "gene_id" be the first two attributes shown
40 - Improved descriptions for thread related errors