TLEN column are all 0s

[lextallan]

Hi!

I'm having an issue when outputting paired end data in SAM/BAM format, where the TLEN column (column 9) are all 0s. I've tested this and had similar issues in 0.2.1 and 0.2.3. This makes it incompatible for some downstream software that relies on the column. Is this working as intended/ is there an issue on my end that could be causing this?

Thanks for any help and for creating such a great tool!

[haowenz]

"It is set as 0 for a single-segment template or when the information is unavailable (e.g., when the first or last segment of a multi-segment template is unmapped or when the two are mapped to different reference sequences)."

We didn't calculate this for now. Initially, Chromap was not optimized for generating SAM output. But we are working on improving SAM format output. The issue you have will be resolved in next release.

[swiftgenomics]

Please check the new release. These tags in SAM are now supported.