options

[smangul1]

check if the extension is bam if bam was selected
right now if i run

~/anaconda2/bin/python imrep.py --noCast example/toyExample.fastq test

this error

Traceback (most recent call last):
File "imrep.py", line 1096, in
imrep = ImReP(settings)
File "imrep.py", line 394, in init
self.__read_reads()
File "imrep.py", line 497, in __read_reads
while not file_content[0][0] == ">":
IndexError: list index out of range