validateManifest (vm) Versions Log

1.9 (RELEASED)
    Added bedMethyl format (just a copy of bedRrbs with a different name)
    Added support for plain BED (non-bigBed) types by using the usual format with a "bed_" prefix.
    Added bedLogR format.
    Allow dm3, dm6 and ce10 assemblies.

1.8 (RELEASED)
    Support for bedRrbs format including bedRrbs.as
    Tolerate phiX174 phage in bams by adding the sequence to encValData/hg19/{chrom.sizes,hg19.2bit}

1.7 (RELEASED)
    Better checks for idat and rcc formats by refactoring the checking code from edwSubmit into hg/lib/encode3/encode3Valid.c.
    New vf version is now 4.7 and tolerates leading blank lines in fastq which covers also the case of trailing blank lines. 
    Checks for enriched_in allowed values by refactoring the checking code from edwSubmit into hg/lib/encode3/encode3Valid.c.
    Fixed error message that reported "experiment" when it was really "replicate".
    Dis-allow these extensions generally: .tgz .tar .tar.gz .zip .bz2
    For .gz only allow format fastq
    For fastq: only allow .gz
    Add single quotes around the fileName output so trailing spaces are visible in the error message.
    Add checks for blank strings for ucsc_db and output_type.
    Add --help option to show usage.
    Restrict replicate small number to 1 to 10 only (for now).
    Add a new optional column technical_replicate that has the same behavior as replicate.
    Add a new optional column paired_end that accepts 1(forward) 2(reverse) or "n/a".
    Add check that format is not blank.