Chirag Jain comments

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                                            Chirag Jain

boolean spgemm: can I avoid numeric phase?

Thanks for responding. I too realized this when I read through the code to have a better understanding of the symbolic phase (both uncompressed and compressed modes). Storing column indices...

PacBio CLR reads

Yes, check the help page `winnowmap -h`

aligning HiFi reads to single pass long reads

This may not be a good use-case for Winnowmap. `map-ont` or `asm20` presets are designed to map reads to a reference/assembly in both Winnowmap and minimap2. Each read is expected...

failed to parse the FASTA/FASTQ record

Can you also try minimap2 and see if the same warning is shown?

failed to parse the FASTA/FASTQ record

Also, you may want to check the fastq file record to make sure it's properly formatted One read is probably left unmapped in SAM file as per this warning.

Mapping using PacBio CCS BAM file

PacBio BAM files are not supported as input currently. That said, do you know any long read mapper that does it? I could consider incorporating this feature if this is...

Winnowmap for read overlapping

The weighted minimiser idea can be extended for read overlapping as well, but we have never tested. It should be easy to add back these options in [options.c](https://github.com/marbl/Winnowmap/blob/master/src/options.c); but testing...

How to map with pre-built indexes ?

See #29

How to change the mapQ and τ？

See `min_mapq` parameter in [options.c](https://github.com/marbl/Winnowmap/blob/master/src/options.c). Currently this is not exposed via command line.

Winnowmappy

Hi @marcus1487 I'm happy to investigate this. But I wonder if it would be a worthwhile exercise at your end to verify whether Winnowmap is giving you desirable improvements first...