Error when using CRAM file as input

[fgvieira]

When running TIDDIT with a CRAM file, i get the error:

BAM file has no @HD SO:<SortOrder> attribute: it is not possible to determine the sort order
Traceback (most recent call last):
  File "/services/tools/tiddit/2.7.0/TIDDIT.py", line 65, in <module>
    TIDDIT_calling.cluster(args)
  File "TIDDIT_calling.py", line 190, in TIDDIT_calling.cluster
    coverage_data=TIDDIT_coverage.coverage(args)
  File "TIDDIT_coverage.py", line 8, in TIDDIT_coverage.coverage
    for line in open(args.o+".tab"):
IOError: [Errno 2] No such file or directory: 'OUTPUT.tab'

Looking a bit more, it seems that it is the cov module that fails, even though the CRAM file has the attribute:

@HD     VN:1.6  SO:coordinate

Does TIDDIT support CRAM files?
thanks,

[J35P312]

Hello there!
That is correct, Tiddit only support Bam file. I will add cram support, but i need to make some larger changes to Tiddit first (it uses the bamtools api, that do not support cram).

Sorry for the messy error message, that one i can fix easier!
//Jesper