Prepend chromosomes with chr to match the SAM/BAM files. #132
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Sorry, I'm terrible and added a separate commit on to this cosmetic one. If you like one and not the other feel free to ignore one of them. |
| Y 9196964 9197108 Y-9196963-9197108 0 + Y-CCDS59533.1 Y-TSPY8 0.0 0.0 | ||
| Y 9197216 9197296 Y-9197215-9197296 0 + Y-CCDS59533.1 Y-TSPY8 0.0 0.0 | ||
| Y 9197992 9198013 Y-9197991-9198013 0 + Y-CCDS59533.1 Y-TSPY8 0.0 0.0 | ||
| chr#{"group_id": null, "sample_id": "tiriwiro", "coverage_source": "/Users/robinandeer/Projects/clinical-genomics/qxt/bam/Sample_E2-QXT-prep2/sorted.bam", "cutoff": 10, "extension": 0} |
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This leading "chr" must be a mistake, right? 😃
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Thanks a lot @roryk - good catch! I'll be happy to test the PR locally after you've made the few suggested changes If you have time you could also update the |
apply_bed_stream takes a function and a BED stream applies the function to every interval in the BED stream Also fixes the test BED file not having chr prepended to the chromosome.
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Superb Rory! Very nice touch with the rebase - I should keep learning more about how to do that And I wonder what it say of me if I'm blushing a little reading you last comment? 😅 Thanks! |
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Hi Robin,
The demo was failing because the chromosome names didn't match up with the alignment files. This fixes that. Hope you are well.