Multifasta references not handled in the PhiPack bed file (parsnp.rec); parsnp 2.1.4

[sconlan]

Since v 2.1.3, parsnp has handled multi-fasta references a produces a vcf with the correct CHROM labels. It seems like the bed file produced by running PhiPack (--recomb-filter) doesn't support this yet.

11:08 cn4325 clade1$ tail parsnp.rec 
1       12308168        12308268        REC     0.000   +
1       12328295        12328395        REC     0.000   +
1       12333736        12333836        REC     0.000   +
1       12337892        12337992        REC     0.000   +
1       12349452        12349552        REC     0.000   +
1       12366020        12366120        REC     0.000   +
1       12379228        12379328        REC     0.000   +
1       12385718        12385818        REC     0.000   +
1       12395554        12395654        REC     0.000   +
1       12404985        12405085        REC     0.000   +