bams2correlation - renamed to bam_vs_bam
pipeline_windows - added cpg stats
bam_vs_bam.py - added regex-identifier
bam2stats.py - updated test
chain2stats.py - added tests, using stdin
test_scripts.py - added manifest option
bam2bed.py - fixed stdin input, fixed tests
bam2fastq.py - fixed tests
Merge branch 'master' of ssh://github.com/CGATOxford/cgat