expanded to 10M and 20M the nonredundant fraction
Merge branch 'develop' of http://frankfurt.aecom.yu.edu/git/wasp/blessedRepository into develop
Merge branch 'develop' into replicatesUpdate
Merge branch 'develop' of http://frankfurt.aecom.yu.edu/git/wasp/blessedRepository into develop
Merge branch 'develop' into replicatesUpdate
nrf expanded to have 2M, 5M, 10M, and 20M, as well as all. Next is to test it
modified the non-redundant read fraction for 20, 10, 5, and 2 million reads, as a command was unexpectedly crashing on the cluster; was resolved by adding a separate command rather than using a pipe. I shall now test it on barcelona
Merge branch 'develop' of http://frankfurt.aecom.yu.edu/git/wasp/blessedRepository into develop
Merge branch 'develop' into replicatesUpdate
got NRF for all reads the new way. will now test
Merge branch 'develop' of http://frankfurt.aecom.yu.edu/git/wasp/blessedRepository into develop
Merge branch 'develop' into replicatesUpdate
fixed naming error in samtools.java; inadvertantly named two files the same. is now fixed and will be tested
Merge branch 'develop' of http://frankfurt.aecom.yu.edu/git/wasp/blessedRepository into develop
Merge branch 'develop' into replicatesUpdate
added quotes around filename for awk command in samtools.java. Also began dealing with genome size bandwidth, and tagSize in Macstwo.java - but this part not complete. Will test the samtools nrf now
nfr now ok; display for its data looks ok
minor
removed bandwith and genomeSize from parameters of the macs2 software. genomeSize will now be derived from sampleMeta species and bandwidth will now be derived from sampleMeta chipseq.fragmentSize (sonication size).
added all (well, nearly all) options for macs2, with tooltips from MAC2 descriptsion, as well as constraints. These are all set to the default values provided in the description.NEXT, will want to use them in macs2 plugins, but only if they differ from the default values.