Comments (3)
mktrost
commented on August 13, 2024
I added an option to turn off the ReadName validation. That fix is in the current master branch.
It was fixed in commit: 9d3eec0
If you update to the current version, and specify "--noRNValidate" it should not enforce alphanumeric sorting. Alternatively, you can modify bamUtil/src/ClipOverlap.cpp and remove the call to "samIn.setSortedValidation(SamFile::QUERY_NAME);"
I hope that fixes your issue. Let me know if you have any questions.
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bjkelly
commented on August 13, 2024
Thank you!
We'll update, test it out, and follow up with how its working.
Ben
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bjkelly
commented on August 13, 2024
Your update seems to be working as advertised. Thank you!
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Related Issues (20)
- Building bamUtil returns error: call of overloaded 'to_string(int&)' is ambiguous HOT 4
- Compile error HOT 4
- Building bamUtil returns error: undefined reference HOT 4
- Cut middle of reads HOT 2
- `bam diff` should exit with a return code
- Dedup does not work from std/in HOT 2
- Cannot Compile NonPrimaryDedup Branch HOT 5
- cannot consume -.ubam on a pipe HOT 2
- Makefile should not ignore system LDFLAGS
- `bam diff` seems to return the reads that look identical between A and B HOT 1
- the clang compiler does not support -pg option on versions of OS X 10.9 and later HOT 4
- Error building from source: libStatGen HOT 3
- BamUtil: recab error: failed to open reference genome HOT 6
- bam2FastQ generates empty fastq files
- bash -x testBam2FastQ.sh and bash -x testMergeBam.sh failed on centos8_aarch64
- can not install with conda HOT 2
- bamutil diff - Get record for every read being compared HOT 2
- build is broken due to deprecated git protocol HOT 1
- Odd stats reported for clipOverlap
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