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Clarify this is a fork in the main help text (#4)
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clintval authored Sep 20, 2024
1 parent 31fdac3 commit 580cab0
Showing 1 changed file with 5 additions and 3 deletions.
8 changes: 5 additions & 3 deletions main.c
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@
#include "utils.h"

#ifndef PACKAGE_VERSION
#define PACKAGE_VERSION "0.7.18-r1243-dirty"
#define PACKAGE_VERSION "0.7.18-r1243-1"
#endif

int bwa_fa2pac(int argc, char *argv[]);
Expand All @@ -57,14 +57,16 @@ static int usage()
{
fprintf(stderr, "\n");
fprintf(stderr, "Program: bwa (alignment via Burrows-Wheeler transformation)\n");
fprintf(stderr, "Fork: This fork of bwa supports interactive `bwa aln`\n");
fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
fprintf(stderr, "Contact: Heng Li <[email protected]>\n\n");
fprintf(stderr, "Contact: Fulcrum Genomics LLC <[email protected]>\n\n");
fprintf(stderr, "Usage: bwa <command> [options]\n\n");
fprintf(stderr, "NOTE: For Bioconda installs replace `bwa` with `bwa-aln-interactive`\n\n");
fprintf(stderr, "Command: index index sequences in the FASTA format\n");
fprintf(stderr, " mem BWA-MEM algorithm\n");
fprintf(stderr, " fastmap identify super-maximal exact matches\n");
fprintf(stderr, " pemerge merge overlapping paired ends (EXPERIMENTAL)\n");
fprintf(stderr, " aln gapped/ungapped alignment\n");
fprintf(stderr, " aln gapped/ungapped alignment (interactive)\n");
fprintf(stderr, " samse generate alignment (single ended)\n");
fprintf(stderr, " sampe generate alignment (paired ended)\n");
fprintf(stderr, " bwasw BWA-SW for long queries (DEPRECATED)\n");
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