Releases: wdecoster/cramino
v0.15.0
Fix for NM (AUX)
This fix support AUX I8, as reported (once more) in #24
fix for PS (AUX::i16)
This release fixes the new problem reported in #24
Now the Aux::I16 and I8 are also supported for the PS tag.
fix for PS (AUX::i32)
This fix addresses the issue reported in #24
modal accuracy, faster cram parsing, fix for stdin, remote files, deprecating checksum
This release adds modal accuracy to the output, is faster to parse crams (probably 2x), includes a fix by @mbhall88 to read from stdin, and can run on remote files (using an HTTPS, FTP, or s3 URL). Calculating a checksum is now deprecated, but please let me know if you thought that was useful, and I will put it back in.
Contributors
Assets 5
Fix karyotype with underscores
This release contains a fix from @Adoni5, removing a filter that kept contigs with an underscore out of the karyotype (#20 and #21). Unplaced contigs (using an ensembl genome) will also be part of the karyotype, as there is no good way to filter those out. Possibly users could, in the future, optionally specify a file with chromosomes they want to see in the karyotype, but that is not yet supported or planned.
Additionally, there is a fix to no longer subtract the softclipped sequences from the read length when running in --ubam mode.
Contributors
Assets 2
Bugfix: ignore softclipped bases
This release fixes a glaring problem: softclips were included when gathering read lengths, which especially for ultralong reads with more supplementary alignments, is a problem, especially after aligning with minimap2 -Y (as is the default in dorado). Thanks to @mattloose for the detective work!
Contributors
Assets 5
Better histograms
This release has better* histograms, with a standardized number of bins and bin sizes.
*if you disagree, let me know
Support ubam
This release also adds N75 and yield for reads >25kb.
Another release
This is another release, including the --spliced option.