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updated sequence-formats dependency allows more lenient parsing of pileup-data, now also allowing for arbitrary reference alleles (not just ACTGN). This won't affect calling (reads that support an allele that is not in the SNP-file input are treated as before), but will be less disruptive when parsing pileup-input, for example without a bed-file in samtools.
improved error output for parsing problems with pileup-format data. Now only a small part of the problematic chunk is output, hopefully easing error interpretation in such cases
output a useful error message if the number of samples passed in --sampleNames is inconsistent with the pileup-input
--samplePopName now accepts multiple pop-names, separated by comma. The number of pop-names must then match the number of samples.