Closed IanSudbery closed 4 years ago
Looks good to me. However, I thought that you were going to warn users rather than error?
The error is for if the interval is invalid for an unknown reason. Lines 476, 477 and 480 deal with overhanging intervals.
Ah ok, I see now.
Can this be merged @IanSudbery?
Yes
Addresses #36 and #67.
Mostly completing the changes so that bam2geneprofile uses pyBigWig rather than bx-python.
Also adds routines that checks if the requested intervals were
Currently going off the 5' end of the contig is checked by the the (Gene/UTR/Intron etc)Counters, while the 3' is only checked in IntervalCounterBigWig. 3' ends should probably be checked for BAM based counting as well (3' ends can't be checked for Bed based counting).
Currently the Signal file backed counters are the only ones with access to the contig sizes. This makes sense, because whether or not they are available depends on the type of file backing them. The interval backed counters are the ones that know if an interval is a primary interval or a flank.
Both 3' and 5' checks should be moved to one or the other, and extended to all file types (where possible). But not clear how to do this.