From 123aceb6a6300fcb092672f57f70fb00cd660022 Mon Sep 17 00:00:00 2001
From: zzh <zzhofhust@gmail.com>
Date: Tue, 2 Apr 2024 07:49:38 +0800
Subject: [PATCH] =?UTF-8?q?=E5=B0=86fmt=E5=92=8Ckmer=E5=90=88=E5=B9=B6?=
 =?UTF-8?q?=E5=88=B0=E5=BB=BA=E7=B4=A2=E5=BC=95=E7=9A=84=E8=BF=87=E7=A8=8B?=
 =?UTF-8?q?=E4=B8=AD?=
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---
 bwtindex.c | 14 +++++++++++---
 main.c     |  2 ++
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/bwtindex.c b/bwtindex.c
index 5973332..cf07e8a 100644
--- a/bwtindex.c
+++ b/bwtindex.c
@@ -230,7 +230,7 @@ int bwa_bwt2bytesa(int argc, char *argv[]) // the "bwt2bytesa" command
 int bwa_bwt2fmt(int argc, char *argv[]) // create fmt index
 {
 	bwt_t *bwt;
-	char buf[1024];
+	//char buf[1024];
 	if (optind + 1 > argc) {
 		fprintf(stderr, "Usage: fastbwa bwt2fmt <in.bwt> <out.fmt>\n");
 		return 1;
@@ -369,14 +369,22 @@ int bwa_idx_build(const char *fa, const char *prefix, int algo_type, int block_s
 		bwt_dump_sa(str3, bwt);
 		bwt_destroy(bwt);
 		if (bwa_verbose >= 3) fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
-		{ 
+		{
+			t = clock();
 			// build FMT-Index
 			FMTIndex *fmt;
 			strcpy(str, prefix); strcat(str, ".fmt");
 			fmt = create_fmt_from_bwt(bwt);
 			dump_fmt(str, fmt);
 			// create Kmer-Hash
-
+			fmt_create_kmer_index(fmt);
+			strcpy(str, prefix); strcat(str, ".kmer");
+			fmt_dump_kmer_idx(str, &fmt->kmer_hash);
+			if (bwa_verbose >= 3) fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
+			// create byte sa
+			bwt_cal_byte_sa(bwt, 4);
+			strcpy(str, prefix); strcat(str, ".bytesa");
+			bwt_dump_byte_sa(str, bwt);
 		}
 	}
 	free(str3); free(str2); free(str);
diff --git a/main.c b/main.c
index 86b8ab1..718e7c0 100644
--- a/main.c
+++ b/main.c
@@ -80,6 +80,8 @@ static int usage()
 	fprintf(stderr, "         bwtupdate     update .bwt to the new format\n");
 	fprintf(stderr, "         bwt2sa        generate SA from BWT and Occ\n");
 	fprintf(stderr, "         bwt2bytesa    generate SA(using byte array) from BWT and Occ\n");
+	fprintf(stderr, "         bwt2fmt       generate FMT-Index from BWT\n");
+	fprintf(stderr, "         buildkmer     generate kmer index from FMT\n");
 	fprintf(stderr, "\n");
 	fprintf(stderr,
 "Note: To use BWA, you need to first index the genome with `bwa index'.\n"