Used .endswith() methods on output file name in add-tag command. Deleted the get_format function.
The logic now is like: if the output filename ends with .bam or .bam.sorted, then generate a bam file; elif it ends with .sam, then generate a sam file; otherwise print an "unknown" prompt and generate a bam file by default.
Used
.endswith()methods on output file name inadd-tagcommand. Deleted theget_formatfunction.The logic now is like: if the output filename ends with
.bamor.bam.sorted, then generate abamfile; elif it ends with.sam, then generate asamfile; otherwise print an "unknown" prompt and generate abamfile by default.