Fixed a typo in rsem-calculate-expression's document; Added multi-thread and memory options to samtools sort thanks to Dr. Samuel Arvidsson
Added support for allele-specific expression estimation
Modified the shebang line for perl scripts
Added '--seed' option for 'rsem-simulate-reads'
 Modified the transcript extraction behavior of 'rsem-prepare-reference'. For transcripts that cannot be extracted, instead of failing the whole script, warning information is produced. Those transcripts are ignored