added filename to match for finding existing chunks . This is needed because chunks from multiple readgroups and lanes can be in the existing chunks dir.
added gettters and setters for file name to match. Added Sample bam to list of possible targets. Creation of job file (*.sh) and log file now is not next to the input fastq but next the output bam for Illuminamem fastq chunks.
for Illumina data with existing fastq chunks the check on if the number of reads in fastq and bam are equal is skipped. This is because the reads in the fastq are not known by the program. Maybe parse this from number of reads from bcl converter output.
added default mark to qualfile beginning. So reset to start also works when no header is present that has to be skipped.