igv_reports fails on chrM

[zmaroti]

At fasta.py line 49:

start = region["start"] - 1 if region["start"] is not None else None
start will result as -1 for chrM variants, then the exception is caught at line 53:

            try:
                seq = self.fasta.fetch(chr, start, end)

Traceback (most recent call last):
File "/home/gdl/.local/bin/create_report", line 8, in
sys.exit(main())
File "/home/gdl/.local/lib/python3.6/site-packages/igv_reports/report.py", line 630, in main
create_report(args)
File "/home/gdl/.local/lib/python3.6/site-packages/igv_reports/report.py", line 133, in create_report
session_dict = json.dumps(create_session_dict(args, table, trackjson))
File "/home/gdl/.local/lib/python3.6/site-packages/igv_reports/report.py", line 288, in create_session_dict
data = sequence_reader.slice(regionSeq)
File "/home/gdl/.local/lib/python3.6/site-packages/igv_reports/fasta.py", line 56, in slice
seq = self.fasta.fetch(chr, start, end)
File "pysam/libcfaidx.pyx", line 288, in pysam.libcfaidx.FastaFile.fetch
File "pysam/libcutils.pyx", line 259, in pysam.libcutils.parse_region
ValueError: start out of range (-1)

I am not sure how it can happen as at report.py start is max(1, start-500)

            regionSeq = (
                {"chr": region["chr"], "start": max(1, region["start"] - 500), "end": region["end"] + 500}
                if region.get("start") is not None
                else region
            )
            data = sequence_reader.slice(regionSeq)

However with a quick hack at fasta.py

         if start < 0:
             start = 0

The error goes away.