From 545fb87feb5c4ff87b3e2c449f9571581abe89b8 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Fri, 22 Feb 2013 17:15:57 -0500
Subject: [PATCH] removed another part related to color-space

---
 bwtmisc.c | 51 ---------------------------------------------------
 main.c    |  2 --
 main.h    |  1 -
 3 files changed, 54 deletions(-)

diff --git a/bwtmisc.c b/bwtmisc.c
index c35d684..de96dc2 100644
--- a/bwtmisc.c
+++ b/bwtmisc.c
@@ -157,57 +157,6 @@ int bwa_bwtupdate(int argc, char *argv[])
 	return 0;
 }
 
-const int nst_color_space_table[] = { 4, 0, 0, 1, 0, 2, 3, 4, 0, 3, 2, 4, 1, 4, 4, 4};
-
-/* this function is not memory efficient, but this will make life easier
-   Ideally we should also change .amb files as one 'N' in the nucleotide
-   sequence leads to two ambiguous colors. I may do this later... */
-uint8_t *bwa_pac2cspac_core(const bntseq_t *bns)
-{
-	uint8_t *pac, *cspac;
-	bwtint_t i;
-	int c1, c2;
-	pac = (uint8_t*)calloc(bns->l_pac/4 + 1, 1);
-	cspac = (uint8_t*)calloc(bns->l_pac/4 + 1, 1);
-	fread(pac, 1, bns->l_pac/4+1, bns->fp_pac);
-	rewind(bns->fp_pac);
-	c1 = pac[0]>>6; cspac[0] = c1<<6;
-	for (i = 1; i < bns->l_pac; ++i) {
-		c2 = pac[i>>2] >> (~i&3)*2 & 3;
-		cspac[i>>2] |= nst_color_space_table[(1<<c1)|(1<<c2)] << (~i&3)*2;
-		c1 = c2;
-	}
-	free(pac);
-	return cspac;
-}
-
-int bwa_pac2cspac(int argc, char *argv[])
-{
-	bntseq_t *bns;
-	uint8_t *cspac, ct;
-	char *str;
-	FILE *fp;
-
-	if (argc < 3) {
-		fprintf(stderr, "Usage: bwa pac2cspac <in.nt.prefix> <out.cs.prefix>\n");
-		return 1;
-	}
-	bns = bns_restore(argv[1]);
-	cspac = bwa_pac2cspac_core(bns);
-	bns_dump(bns, argv[2]);
-	// now write cspac
-	str = (char*)calloc(strlen(argv[2]) + 5, 1);
-	strcat(strcpy(str, argv[2]), ".pac");
-	fp = xopen(str, "wb");
-	fwrite(cspac, 1, bns->l_pac/4 + 1, fp);
-	ct = bns->l_pac % 4;
-	fwrite(&ct, 1, 1, fp);	
-	fclose(fp);
-	bns_destroy(bns);
-	free(cspac);
-	return 0;
-}
-
 int bwa_bwt2sa(int argc, char *argv[])
 {
 	bwt_t *bwt;
diff --git a/main.c b/main.c
index fc63c2e..dbe9dd0 100644
--- a/main.c
+++ b/main.c
@@ -27,7 +27,6 @@ static int usage()
 	fprintf(stderr, "         pac2bwtgen    alternative algorithm for generating BWT\n");
 	fprintf(stderr, "         bwtupdate     update .bwt to the new format\n");
 	fprintf(stderr, "         bwt2sa        generate SA from BWT and Occ\n");
-	fprintf(stderr, "         pac2cspac     convert PAC to color-space PAC\n");
 	fprintf(stderr, "\n");
 	return 1;
 }
@@ -52,7 +51,6 @@ int main(int argc, char *argv[])
 	else if (strcmp(argv[1], "aln") == 0) ret = bwa_aln(argc-1, argv+1);
 	else if (strcmp(argv[1], "samse") == 0) ret = bwa_sai2sam_se(argc-1, argv+1);
 	else if (strcmp(argv[1], "sampe") == 0) ret = bwa_sai2sam_pe(argc-1, argv+1);
-	else if (strcmp(argv[1], "pac2cspac") == 0) ret = bwa_pac2cspac(argc-1, argv+1);
 	else if (strcmp(argv[1], "bwtsw2") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
 	else if (strcmp(argv[1], "dbwtsw") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
 	else if (strcmp(argv[1], "bwasw") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
diff --git a/main.h b/main.h
index 7b638ca..3e70362 100644
--- a/main.h
+++ b/main.h
@@ -6,7 +6,6 @@ extern "C" {
 #endif
 
 	int bwa_fa2pac(int argc, char *argv[]);
-	int bwa_pac2cspac(int argc, char *argv[]);
 	int bwa_pac2bwt(int argc, char *argv[]);
 	int bwa_bwtupdate(int argc, char *argv[]);
 	int bwa_bwt2sa(int argc, char *argv[]);