1.5.5 - Bug fix to allow dual index on casava format

Bug fix for casava barcode/index, had to deal with some deprecations

Correct range for Illumina 1.5+

Include ASCII 66 -> 2 for Illumina 1.5+ when determining quality score format:

If a read ends with a segment of mostly low quality (Q15 or below), then all of the quality values in the segment are replaced with a value of 2 (encoded as the letter B in Illumina's text-based encoding of quality scores)... This Q2 indicator does not predict a specific error rate, but rather indicates that a specific final portion of the read should not be used in further analyses.

1.5.3: filenames for CWL compat

+ is not allowed in file names anymore, as CWL could not "glob" an output with a + in its name

1.5.0 merged Seq Protocol to Data Type, CASAVA 1.8 compatibility

• IMPORT 1.0 changed to merge Seq Protocol and Data Type
• Compatible with FastQs in CASAVA 1.8 format

1.4.2 - bz2 compressed FastQ support

• added function to process bz2 compressed FastQ format.

1.4.1 - Minor file name extensions check fix

• validator now allows upper cases in FastQ file name extensions.

1.3.0 - please upgrade

• Fixes valid_q value of seq-valid json report. Always returned false previously.
• Correct command line help text for seq-valid input option.
• Extends the seq-valid json report to include the ascii range detected and which types of
  phred score these align to.
• Additional command line options for seq-valid
  • -o | --output - Generates an interleaved gzip compressed fastq file when input is paired fastq
  • -q | --qc - Specify the number of pairs to be used when assessing the phred quality range
    • Added for performance reasons

Informative exceptions

Catch low level exceptions and raise as informative errors

Mainly changes to test framework and command line

Now uses subcommands to simplify use. Base command is now cgpSeqInputVal see README.md for details.