csf-ngs / fastqc

csf fork of fastqc for usage on selected reads of unaligned bam file

###private fork of fastqc (0.10.0)

added a read argument for unaligned bam files. probably breaks other file types, but I don't care.

#####call with: fastqc-csf/fastqc --read {d} file.bam

where {d} is:

• 0: unaligned bam file with one read only (4 in flags)
• 1: unaligned bam file with paired end reads. Takes only 1. read
• 2: unaligned bam file with paired end reads. Takes only 2. read

#####build:

1. ant deploy.
2. copy the fastqc-csf folder to your destination.