cannot use absolute path in ReadExtractor

[jinyung]

Hi Inigo,

I think this is inconvenient to users used to using absolute path in their script:

Circle-Map/circlemap/extract_circle_SV_reads.py

Line 64 in ed88ff6

raw_bam = ps.AlignmentFile(self.working_dir + "/" + self.sorted_bam, "rb")

Circle-Map/circlemap/extract_circle_SV_reads.py

Line 88 in ed88ff6

circle_sv_reads = ps.AlignmentFile(self.working_dir + "/" + self.output_bam , "wb", template=raw_bam)

Best regards
JY

[iprada]

Dear @jinyung,

You are absolutely right. I wish 6 years ago Inigo was a better programmer.

Right now I am busy with other projects, and have limited time to dig into this. Would you be up for making a pull request?

I'll gladly accept one!