error handling w/ insufficient memory

[jamesdalg]

Sometimes, without sufficient ram, quasar crashes. I've encountered this several times. In this case, I'm using 256GB of ram and it's insufficient to generate correct stats for 10kb.
Traceback (most recent call last):
File "/data/CCRBioinfo/dalgleishjl/quasarenv/bin/hifive", line 849, in
main()
File "/data/CCRBioinfo/dalgleishjl/quasarenv/bin/hifive", line 93, in main
run(args)
File "/data/CCRBioinfo/dalgleishjl/quasarenv/lib/python2.7/site-packages/hifive/commands/find_quasar_scores.py", line 134, in run
q1.print_report(args.report)
File "/data/CCRBioinfo/dalgleishjl/quasarenv/lib/python2.7/site-packages/hifive/quasar.py", line 642, in print_report
self._print_txt_report(filename, qscores, rscores)
File "/data/CCRBioinfo/dalgleishjl/quasarenv/lib/python2.7/site-packages/hifive/quasar.py", line 855, in _print_txt_report
temp = [label, self._num2str(cov), "%0.6f" % qscores[-1, i, j]]
IndexError: index 1 is out of bounds for axis 1 with size 1

[msauria]

I agree this is an issue. I will look into improving this.

[jamesdalg]

Also helpful. With 5kb, it takes >1024GB to run. Question-- is there documentation that explains the per chromosome metrics in the text report?

[msauria]

The best thing to do is look at https://www.biorxiv.org/content/early/2017/11/14/204438
The per chromosome metrics are the same as the global metric, as for as calculation. They're less useful unless you're really interested in looking at chromosome variation.