Expected allele lengths, and more
Added: * Added a new section expected_allele_length to the FDSTools library format. In this section, the minimum and (optionally) maximum allele length of each marker can be specified. * Added -L/--check-length option to the TSSV tool. If specified, the tool will use the expected_allele_length values to filter the results. * Samplevis can now truncate long allele names to a given number of characters (defaulting to 70). * Added an option to Samplestats to keep negatives when filtering (abs filter). Changed: * Renamed the --aggregate-below-minimum option of the TSSV tool to --aggregate-filtered. Improved: * Added an option to read_sample_data_file such that other code can request or require that the X_corrected columns are used. * Samplestats will now round to 4 or 5 significant digits if a value is above 1000 or 10000, respectively. * BGHomRaw will no longer round the forward, reverse, and total columns. * When generating mtDNA allele names, FDSTools will now try to avoid creating gaps in the alignment of the sequences against the reference. * Grouped the filtering options of the TSSV tool in its help text. * Cleaned up some leftover code for special sequence value handling (more specifically: code that expected ensure_sequence_format to return False for special sequence values, which it no longer does). * Cleaned up some dead legacy code in reduce_read_counts.