Changes for version 0.02 - 2026-11-11
- Test fixes
- On Windows, t/blood.t, t/concordance.t, t/faidx.t, t/parent.t, t/relatedness.t and t/sex.t failed 19 subtests between them, and t/msa.t would have failed one where Alien::Bioinf is installed. Each test sent STDOUT to a file in text mode, so every "\n" the module printed was "\r\n" in the file, and then read that file back with :raw. The module was right; the tests now read the file in text mode. Found by CPAN Testers reports 620bc624-ddea-11f1-b231-87fe50e89311 (Strawberry Perl 5.24.4) and 666d71f4-ddea-11f1-b231-87fe50e89311 (Strawberry Perl 5.42.3) on 0.01-TRIAL, and reproduced on Linux with PERLIO=:unix:crlf.
- t/pdb.t compared an E-value from its JSON fixture exactly, and JSON::PP 2.97001 under Strawberry Perl 5.24.4 decoded 9.682e-47 as 9.6820000000001e-47, which failed one subtest. The test now allows a relative error of 1e-12, a hundred times what that report showed.
- Bug fixes
- pdb_search's report wrote E-values with three exponent digits ("1.6e-089") on Strawberry Perl 5.24.4, whose C runtime prints them that way, and with two ("1.6e-89") everywhere else. It now writes two on every platform, keeping a third only where the exponent needs it. The same report (620bc624) found it in three subtests of t/pdb.t, which now tests the shortening directly.
Modules
FASTA I/O in XS, BLAST hit ranking, and alignment plots and tables