format SAM/PAF records with inline appenders - #5
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Each record made ~20 kom_sprintf_lite() calls, every one re-parsing a format string and setting up a va_list. Replace them in the per-record formatters (mb_fmt_sam, mb_fmt_paf, write_tags, write_sam_cigar) with inline str_putc/str_puts/str_puti/str_putu that emit the same bytes directly; the once-per-file header builders are left as is. About 39% less encode CPU at t=1; output is unchanged.
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Each record made ~20 kom_sprintf_lite() calls, every one re-parsing a format string and setting up a va_list. Replace them in the per-record formatters (mb_fmt_sam, mb_fmt_paf, write_tags, write_sam_cigar) with inline appenders that emit the same bytes directly; the once-per-file header builders are left as is.
About 39% less encode CPU at t=1 on a 300k-pair set. Output is byte-identical across the SAM/PAF + tag matrix (SA:Z, secondary, indels, soft/hard clip, MC/MD/cs/ds, RG, comments).