added base counts to Cram2Bam bam -c option
changed record and base counts output format in Cram2Bam
added 'prefix' option to Cram2Fastq
Cram2Fastq: fixed read numbering to start from 1
fix for fastq dump failing on external sequences. 
added support for '--reverse' option in fastq dumper.
made sequence URI injection optional.
fixed fastq command for lossy quality scores