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removed another part related to color-space

This commit is contained in:
Heng Li 2013-02-22 17:15:57 -05:00
parent f122fad562
commit 545fb87feb
3 changed files with 0 additions and 54 deletions
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51
bwtmisc.c
View File

@ -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;

2
main.c
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@ -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);

1
main.h
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@ -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[]);