Check: Chromosomes in stats file need to be subset of those in genome (index)

[vinjana]

Chromosomose in the stats file (chromosome lengths ATCG) need to be checked to be a subset of those in the FASTA file/index. If they are not, then probably the workflows is misconfigured. A descriptive error message needs to be thrown. All tools taking the CHROM_SIZES_FILE should do this check. Similarly, alse the CHROMOSOME_INDICES variable of the WGBS workflow should get checked

Failure to check may result in partial statistics or statistics mislabeled, e.g. in case of xenograph alignments, without any error raised. In the worst case these remain unnoticed. Alternatively, an incorrect CHROM_SIZES_FILE may yield an unspecific message from the filter_readbins.pl script (that also occurs in other situations, e.g. if the input is truncated due to pipe-errors).

This should be checked early in the job scripts or earlier, e.g. in checkExecutability() in the Java code. If there is no BAM file yet, it should be checked against the BWA index directly to prevent mapping against the wrong INDEX. For the BWA index the .annfile can be used.

[vinjana]

Check out #23