output SAM without header

[MHryc]

I've ran winnowmap on pbCLR but the output lacks a header (there's only the @pg field). Judging by the stdOut output it finished without error

[M::worker_pipeline::34602.239*29.58] mapped 61546 sequences
[M::worker_pipeline::34669.914*29.58] mapped 60082 sequences
[M::worker_pipeline::34735.371*29.59] mapped 63587 sequences
[M::worker_pipeline::34801.075*29.59] mapped 65496 sequences
[M::worker_pipeline::34864.829*29.59] mapped 68133 sequences
[M::worker_pipeline::34927.821*29.59] mapped 69636 sequences
[M::worker_pipeline::34944.797*29.59] mapped 19214 sequences
[M::main] Version: 2.03, pthreads=48, omp_threads=3
[M::main] CMD: /mnt/storage_2/scratch/pl0217-01/4_MHryc/ref_guided_asm/02_1st_alignment/.pixi/envs/default/bin/winnowmap -W repetitive_k15.txt -ax map-pb-clr --sv-off data/genome.fa.gz data/b2f1.fa.gz
[M::main] Real time: 34945.122 sec; CPU: 1033943.993 sec; Peak RSS: 38.318 GB

[skoren]

This isn't coming from winnowmap but minimap2 on which it is based. When there's a multi-part index, no header is output. See lh3/minimap2#171 for details. The solution is to manually add the header after the fact or increase the -I option.