[imallona]

Parser::fill_up matched a coverage file to its sample by searching the external id anywhere in the file's path. A short id matched longer names and directory names: mes.all.bw was taken for sample es, and under a directory called cores16 every file was. A sample matched to the wrong file dropped out of the sample set, so its junctions were not used for stitching and the parser ran fewer threads.

The id must now be a whole token of the base name, bounded by non-alphanumeric characters, and the longest matching id wins. Two files naming one sample are reported.

On ten samples named es, mes, ir, a3, a5, mee, afe, ale, mixed_terminal and mixed_internal: 9 recognised before, 10 after; junction entries on chr19 go from 125,175 to 137,704.

Tests: ctest, 48 pass, three of them new.