Added user-friendly error messages if users forget to compile the source codes
Fixed a bug that will lead perl scripts fail to find the perl module they use
Modified rsem-tbam2gbam so that the original alignment quality MAPQ will be preserved if the input bam is not from RSEM
Added some user-friendly error messages for BamConverter.h
remove .gitignore from the staging area
Removed a too stringent sanity check in rsem-gen-transcript-plots
Modified my_assert.h to postpone error message string generation
Modified wiggle.cpp & wiggle.h for more accurate floating point number arithmetics. Modified rsem-gen-transcript-plots to output warning messages instead of exit the script when positions where multiread track has less coverage than uniq track are detected. Thanks Han Lin for pointing out the problem and suggesting possible fixes