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One current design limitation of pyfaidx is that it mirrors the samtools indexing behavior of truncating headers after whitespace. There is a good reason for this - any whitespace in the identifier would break the index file. A side effect of this is that frequently the "description" in a header will be lost when reading into the file using the index. It seems like an option to recover the full header line would be useful, and pretty cheap to implement.
To determine the byte offset and length of the header from the index file, we can determine the byte end of the preceding sequence by adding unprintable characters, and this should be the byte start of the real header line. We can then read from header byte start to sequence offset and save this as something like Sequence.long_name.
The text was updated successfully, but these errors were encountered:
One current design limitation of pyfaidx is that it mirrors the samtools indexing behavior of truncating headers after whitespace. There is a good reason for this - any whitespace in the identifier would break the index file. A side effect of this is that frequently the "description" in a header will be lost when reading into the file using the index. It seems like an option to recover the full header line would be useful, and pretty cheap to implement.
To determine the byte offset and length of the header from the index file, we can determine the
byte end
of the preceding sequence by adding unprintable characters, and this should be thebyte start
of the real header line. We can then read from headerbyte start
to sequenceoffset
and save this as something likeSequence.long_name
.The text was updated successfully, but these errors were encountered: