Fixed a minor bug which only affects paired-end reads for reporting how many alignments are processed when RSEM generates BAM outputs
Renamed --phred33-quals, --phred64-quals, and --solexa-quals to --bowtie-phred33-quals, --bowtie-phred64-quals, and --bowtie-solex-quals to avoid confusion
Added support for DE analysis on multiple conditions via running EBSeq
'rsem-run-ebseq': Added 'output_file.condmeans' for tests with more than 2 conditions
Changed WHAT_IS_NEW
Fixed a bug for adding EBSeq's local library path
Fixed loading library problem for EBSeq/install