Bumped versions for develop 1.22-SNAPSHOT
Changed parameters READ_DESCRIPTOR and ANNOTATION_MAPPING and added READ_STRAND
AnnotationMapper gets read descriptor as argument in constructor - avoid null with BAM files
Fixed bug when reading alignment blocks multiple times
Fixed bug when calculating blocks length
BARNA-273 - Implemented stranded annotation mapping for BAM files
Added test for splice junction count on stranded data
BARNA-293 - Fixed read count for splice junctions and introns on stranded data
Not using flag 0x100 for counting the number of read in BAM files
Fixed block test
Set locale US for Windows on the whole class
Getting commandline parameters from settings using JSAPParameters helper class
Added return value to Parameter parse() method
Removed the coverage_stats paramter and reduced to coverage file
Changed dependency of BiasProfiler
Fixed some tests and BARNA-296
BARNA-297 - removed the append parameter for stats and removed the file locking
Removed the gtf line skip waring printout and moved the single example to the read stats printer
minor fix to make sure base for RPKM is never 0
Merge branch 'develop' of http://sammeth.net/fisheye/git/barna into develop
Moved coverage stats log out of the loop
added value description to sam validation stringency