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| var countNinDepth *bool = coverageFlags.Bool("countNinDepth", true, "If true, count 'N' reads towards total depth of pileups.") | ||
| var verbose *int = coverageFlags.Int("verbose", 0, "Set to 1 to reveal debug prints. Verbose in this program reports Poisson parameter lambda.") | ||
| var highEndFilter *float64 = coverageFlags.Float64("highEndFilter", 0.001, "Percent threshold from right end of distribution to be filtered out") | ||
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This is to fix a bug in the "coverage" subcommand where the optional arguments weren't defined until after the logfatal check for number of arguments. So previously they weren't printed out when the user types ~/go/bin/samInfo coverage
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #1124 +/- ##
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Coverage 66.13% 66.13%
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Files 443 443
Lines 172452 172481 +29
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+ Hits 114049 114070 +21
- Misses 56803 56810 +7
- Partials 1600 1601 +1 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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| //open up the alinment file with a bam reader (more efficient search for overlapped regions) | ||
| br, _ := sam.OpenBam(s.InFile) | ||
| bai := sam.ReadBai(s.InFile + ".bai") |
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Is there a check for the existence of a valid bai file that log fatals if the check fails?
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The ReadBai function would log fatal if the .bai file didn't exist. But I created some safer and more specific error handling. Thanks!
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Description
This is a follow up PR to the one that got merged in yesterday. It adds an option to the saminfo mapq function where the user can specify a bed region and only alignments overlapping that bed region will be analyzed for the mapping quality histogram.
The consequential function to look at is the bedRegionsOnly sub function. All other code should be the same as before, but I had to break it up into multiple sub-functions so that both bedRegionsOnly and the original wholeGenome functions could use the sub functions.
lmk if you have any questions!
🐛 Bug Report
Testing
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Checklist before requesting a review
go fmtormake cleanwas used on all files included