Comments (2)
sergpolly
commented on September 2, 2024
_io.py reveals the secret, I think.
My sym-links didn't have .gz suffix, and thus have been recognized as a simple text file, avoiding the whole pbgzip. That's probably why, header could not go through that step...
Will try that tomorrow - first thing in the morning.
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sergpolly
commented on September 2, 2024
Works like charm , when I make distiller think that input filename wildcard looks like this: pairsam_chunk*.pairsam.gz ...
pairsamtools merge relies on the file suffix to know if it's compressed or not, so make sure you give this info to pairsamtools merge...
Problem solved.
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Related Issues (20)
- What's the difference between "uu' and "UU" in .pairs file? HOT 9
- pipe error with bwa-mem2.avx512bw (2.2.1) HOT 1
- There is no instruction on how to test the project.
- Why reading using pipes rather than another method? HOT 1
- stats redesign HOT 2
- Feature request - split parse from filters HOT 4
- All pairs are corrupt ("XX") HOT 6
- Cannot import name 'dedup_cython' from partially initialized module 'pairtools.lib' (most likely due to a circular import) HOT 7
- parse vs parse2 difference in default behavior for --flip?
- Memory overconsumption/leak (?) in pairtools restrict
- Swap memory overconsumption & program failure during pairtools restrict HOT 1
- Wording in pairtools parse2 for --max-insert-size
- most likely due to a circular import HOT 3
- raise an error/warning if chromosome names in .chrom.sizes and bwa index differ too much
- Updating the ReadTheDocs
- Scaling by pairs error HOT 1
- pairtools parse used name sorted or coodinate sorted bam file as input HOT 2
- pairtools dedup: invalid value encountered in divide HOT 1
- Extracting contact matrices from pairs file HOT 2
- pairtools sort issue HOT 2
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