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Add a bit of doc to cinread cmdline #68

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Merged
jamorrison merged 1 commit into from
Sep 8, 2025
Merged

Add a bit of doc to cinread cmdline #68

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15 changes: 15 additions & 0 deletions src/cinread.c
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Original file line number Diff line number Diff line change
Expand Up @@ -206,6 +206,21 @@ static void usage() {
fputs(tp_names[i], stderr);
} fputs("\n", stderr);
fputs(" [QNAME,QPAIR,BSSTRAND,CRBASE,CQBASE]\n", stderr);
fprintf(" QNAME: read name:")
fprintf(" QPAIR: which read in pair");
fprintf(" STRAND: forward or reverse strand");
fprintf(" BSSTRAND: which original strand the read derives from");
fprintf(" MAPQ: MAPQ score");
fprintf(" QBEG: read start position");
fprintf(" QEND: read end position");
fprintf(" CHRM: chromosome");
fprintf(" CRPOS: cytosine position on reference");
fprintf(" CGRPOS: CpG position on reference (-1 if not applicable)");
fprintf(" CQPOS: cytosine position on read");
fprintf(" CRBASE: cytosine reference base");
fprintf(" CCTXT: cytosine context, strand flipped");
fprintf(" CQBASE: base called on read");
fprintf(" CRETENTION: retention (R) or conversion (C));");
fprintf(stderr, " -s Consider secondary mapping [off]\n");
fprintf(stderr, " -o STR Output file [stdout]\n");
fprintf(stderr, " -h This help\n");
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