seqcounter 1.0.2

Documentation and validation, and one fix to the per-sample report. The counts are unchanged: 1.0.2 and 1.0.1 count identically.

• A Tutorial: counting IS6110 in three public M. tuberculosis read sets, from installing to reading the reports and normalizing the counts, with the real output of every command.
• A Validation page, which bash validation/run_validation.sh reproduces from public data in a few minutes. What it establishes: the counts are identical, read for read, to an independent exact k-mer scan over 200,000 reads and 77 references; a reference is counted once per sequence of a fasta file, even at 16 copies; with even coverage the counts follow the model to a median of 1.00 and recover a 16-copy element as 16.1 copies; a sequence absent from the genome stays at zero everywhere; and -m 1 adds reads from near-matches elsewhere in the genome for 22 of 77 references, by nothing at the median window and up to +43%.
• Three figures, drawn from those same results by validation/make_figures.py: the counts against the model, the spread of real coverage, and a circular map of the H37Rv chromosome showing its 16 IS6110 copies, the 75 single-copy references and the copy number of every kilobase of the genome.
• Fix: refseqcounts_samples.tsv is always one line of eight fields per sample. A tab in an error message (Seal's output is tab aligned, and the message carries the last ten lines of it) or in a file name is replaced by a space, instead of shifting the columns of that row.
• The logo is drawn as outlines rather than text, so it renders without the font it was designed in.

pip install seqcounter   # needs BBTools: conda install -c bioconda bbmap

The full changelog, and the 1.0.0 release for what changed against the first version.