Hi,
this PR addressed issue #25 and adds support for BAM files generated from aligning fasta files rather than fastq.
The functionality is implemented through a command line option -f that instructs pinfish_polish to generate sequence files in fasta instead of fastq. I initially considered implementing autodetection of the format, but it would probably mean basing the decision on the first line of the BAM file and it felt a bit hackish and overly complicated.
I've made the PR against master, but I'm happy to rebase on dev if needed.
bsipos
commented
4 years ago
Hi, this PR addressed issue #25 and adds support for BAM files generated from aligning fasta files rather than fastq.
The functionality is implemented through a command line option
-fthat instructspinfish_polishto generate sequence files in fasta instead of fastq. I initially considered implementing autodetection of the format, but it would probably mean basing the decision on the first line of the BAM file and it felt a bit hackish and overly complicated.I've made the PR against master, but I'm happy to rebase on dev if needed.