The samtools software does not support gzip'ed files, because it can't index gzip-ed files. For instance, if we try to use a gzip'ed FASTA file, we get:
[fai_load] build FASTA index.
Cannot index files compressed with gzip, please use bgzip
Because it supports bgzip, the aroma.seq pathname parser should be updated to recognize *.bgz files too. Until then, we can only work with uncompressed FASTA files.
The samtools software does not support gzip'ed files, because it can't index gzip-ed files. For instance, if we try to use a gzip'ed FASTA file, we get:
Because it supports bgzip, the aroma.seq pathname parser should be updated to recognize
*.bgzfiles too. Until then, we can only work with uncompressed FASTA files.Related to https://github.com/HenrikBengtsson/Costello-PSCN-Seq/issues/5#issuecomment-310870978