Related Issues (20)
- Do extra read checking
- --align-debug flag
- group_on, when the target field is null
- Enforce lack of comma in reference names, and also group_on fields
- Fix duplicated columns in library generation
- Check if discard_nonzero_mismatch is still in use
- Empty string as the feature name?
- Look into why gzip output seems broken
- Update nimble's I/O to always override outputs, rather than append
- Ensure align-debug output contains columns for all information relevant to filtering and decisions
- Implement a reference-library level option for 'max-hits-to-report'
- Sort mult-ref allele hits so the string is deterministic
- Add strandedness filters to alignment pipeline HOT 1
- Move baseline from 0->20 in score filter
- Ensure samtools sort call on the UR flag keeps paired-end reads together HOT 1
- Align should work with files instead of only paths
- Fastq.gz not parsing appropriately HOT 4
- Re-enable --debug
- Add validation to BAM/FASTQ input
- Suggestions for nimble debug/QC report HOT 1
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