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samtools / htslib

C library for high-throughput sequencing data formats
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Extend annot-tsv, adding several new options #1779

Closed pd3 closed 1 month ago

pd3 commented 2 months ago

-d, --delim .. add support for other delimiters, not just tab

-h, --headers .. allow header lines in different formats. This is motivated by the common use of files with the first row containing column names but without the leading # character.

-I, --no-header-idx .. suppress column index numbers in the printed header. When given twice, drops the entire header

--help .. changed from -h, --help to just --help. Note this option was not advertised in the man page nor the usage page, therefore it should be okay to reuse it for -h, --headers.

whitwham commented 1 month ago

Thanks for the memory leak change but the negative header values are still not working.

So (from the tests): annot-tsv -s src.11.txt -t dst.11.txt -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II

gives:

1 10 20 A A 1 30 40 A B 1 50 60 A .

Which is correct, but using the same files: annot-tsv -s src.11.txt -t dst.11.txt -c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II

gives:

1 30 40 A B 1 50 60 A .

So unless I'm using it wrong the first line is going missing.

pd3 commented 1 month ago

Duh, it should work now, sorry