No -I option

[soisa001]

When running winnowmap, the -I option is not recognized.
e.g. after generating the repetitive_k15.txt with meryl:

winnowmap -W repetitive_k15.txt -a -x map-pb -Y -L --eqx --cs -I 32G ref.fa.gz reads.fastq.gz | samtools view -hb | samtools sort -@8 > alignment_sorted.bam

Yields the following error:

[ERROR] unknown option in "-I"

The -I option is needed for a multi-part index.
Thanks.

[cjain7]

Sorry, multi-part indexing is not supported yet.

[diego-rt]

Hi @cjain7

Does this mean that it's not possible to map to genomes larger than 4G while getting accurate mapQs? For minimap2 this would be the case in the absence of the -I flag.

Thanks!

[skoren]

I saw this change was added post the last v2.0.3 release version so the condo-installed versions allow using the -I option. I do see slight differences in alignments when increasing -I on genomes w/>4gb genome size. I wanted to confirm if it is safe to use this option assuming no saved index is used or was it removed because it was not working correctly in v2.0.3 as well?