* added prelimiary VCF parser (not finished)

[samtools.git] / bcftools / bcf.c

diff --git a/bcftools/bcf.c b/bcftools/bcf.c
index e40631975af4351436efdc938c01dca054567c85..aa1bb03d8ee2bbcc035f486a9ba2cc2fcc474a6e 100644 (file)
--- a/bcftools/bcf.c
+++ b/bcftools/bcf.c
@@ -4,8 +4,6 @@
 #include "kstring.h"
 #include "bcf.h"
 
-int bcf_hdr_read(bcf_t *b);
-
 void bcf_hdr_clear(bcf_hdr_t *b)
 {
        free(b->name); free(b->sname); free(b->txt); free(b->ns); free(b->sns);
@@ -22,25 +20,18 @@ bcf_t *bcf_open(const char *fn, const char *mode)
                b->fp = strcmp(fn, "-")? bgzf_open(fn, mode) : bgzf_fdopen(fileno(stdin), mode);
        }
        b->fp->owned_file = 1;
-       if (strchr(mode, 'r')) bcf_hdr_read(b);
        return b;
 }
 
 int bcf_close(bcf_t *b)
 {
-       int ret;
        if (b == 0) return 0;
-       ret = bgzf_close(b->fp);
-       free(b->h.name); free(b->h.sname); free(b->h.txt); free(b->h.ns); free(b->h.sns);
-       free(b);
-       return ret;
+       return bgzf_close(b->fp);
 }
 
-int bcf_hdr_write(bcf_t *b)
+int bcf_hdr_write(bcf_t *b, const bcf_hdr_t *h)
 {
-       bcf_hdr_t *h;
-       if (b == 0) return -1;
-       h = &b->h;
+       if (b == 0 || h == 0) return -1;
        bgzf_write(b->fp, "BCF\4", 4);
        bgzf_write(b->fp, &h->l_nm, 4);
        bgzf_write(b->fp, h->name, h->l_nm);
@@ -52,26 +43,12 @@ int bcf_hdr_write(bcf_t *b)
        return 16 + h->l_nm + h->l_smpl + h->l_txt;
 }
 
-int bcf_hdr_cpy(bcf_hdr_t *h, const bcf_hdr_t *h0)
-{
-       *h = *h0;
-       h->name = malloc(h->l_nm);
-       h->sname = malloc(h->l_smpl);
-       h->txt = malloc(h->l_txt);
-       memcpy(h->name, h0->name, h->l_nm);
-       memcpy(h->sname, h0->sname, h->l_smpl);
-       memcpy(h->txt, h0->txt, h->l_txt);
-       bcf_hdr_sync(h);
-       return 0;
-}
-
-int bcf_hdr_read(bcf_t *b)
+bcf_hdr_t *bcf_hdr_read(bcf_t *b)
 {
        uint8_t magic[4];
        bcf_hdr_t *h;
-       if (b == 0) return -1;
-       bcf_hdr_clear(&b->h);
-       h = &b->h;
+       if (b == 0) return 0;
+       h = calloc(1, sizeof(bcf_hdr_t));
        bgzf_read(b->fp, magic, 4);
        bgzf_read(b->fp, &h->l_nm, 4);
        h->name = malloc(h->l_nm);
@@ -82,8 +59,15 @@ int bcf_hdr_read(bcf_t *b)
        bgzf_read(b->fp, &h->l_txt, 4);
        h->txt = malloc(h->l_txt);
        bgzf_read(b->fp, h->txt, h->l_txt);
-       bcf_hdr_sync(&b->h);
-       return 16 + h->l_nm + h->l_smpl + h->l_txt;
+       bcf_hdr_sync(h);
+       return h;
+}
+
+void bcf_hdr_destroy(bcf_hdr_t *h)
+{
+       if (h == 0) return;
+       free(h->name); free(h->sname); free(h->txt); free(h->ns); free(h->sns);
+       free(h);
 }
 
 static inline char **cnt_null(int l, char *str, int *_n)
@@ -105,7 +89,10 @@ static inline char **cnt_null(int l, char *str, int *_n)
 int bcf_hdr_sync(bcf_hdr_t *b)
 {
        if (b == 0) return -1;
-       b->ns = cnt_null(b->l_nm, b->name, &b->n_ref);
+       if (b->ns) free(b->ns);
+       if (b->sns) free(b->sns);
+       if (b->l_nm) b->ns = cnt_null(b->l_nm, b->name, &b->n_ref);
+       else b->ns = 0, b->n_ref = 0;
        b->sns = cnt_null(b->l_smpl, b->sname, &b->n_smpl);
        return 0;
 }
@@ -161,7 +148,7 @@ int bcf_sync(int n_smpl, bcf1_t *b)
        return 0;
 }
 
-int bcf_write(bcf_t *bp, const bcf1_t *b)
+int bcf_write(bcf_t *bp, const bcf_hdr_t *h, const bcf1_t *b)
 {
        uint32_t x;
        int i, l = 0;
@@ -173,18 +160,18 @@ int bcf_write(bcf_t *bp, const bcf1_t *b)
        bgzf_write(bp->fp, b->str, b->l_str);
        l = 12 + b->l_str;
        for (i = 0; i < b->n_gi; ++i) {
-               bgzf_write(bp->fp, b->gi[i].data, b->gi[i].len * bp->h.n_smpl);
-               l += b->gi[i].len * bp->h.n_smpl;
+               bgzf_write(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
+               l += b->gi[i].len * h->n_smpl;
        }
        return l;
 }
 
-int bcf_read(bcf_t *bp, bcf1_t *b)
+int bcf_read(bcf_t *bp, const bcf_hdr_t *h, bcf1_t *b)
 {
        int i, l = 0;
        uint32_t x;
        if (b == 0) return -1;
-       if (bgzf_read(bp->fp, &b->tid, 4) == 0) return 0;
+       if (bgzf_read(bp->fp, &b->tid, 4) == 0) return -1;
        bgzf_read(bp->fp, &b->pos, 4);
        bgzf_read(bp->fp, &x, 4);
        b->qual = x >> 24; b->l_str = x << 8 >> 8;
@@ -195,10 +182,10 @@ int bcf_read(bcf_t *bp, bcf1_t *b)
        }
        bgzf_read(bp->fp, b->str, b->l_str);
        l = 12 + b->l_str;
-       bcf_sync(bp->h.n_smpl, b);
+       bcf_sync(h->n_smpl, b);
        for (i = 0; i < b->n_gi; ++i) {
-               bgzf_read(bp->fp, b->gi[i].data, b->gi[i].len * bp->h.n_smpl);
-               l += b->gi[i].len * bp->h.n_smpl;
+               bgzf_read(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
+               l += b->gi[i].len * h->n_smpl;
        }
        return l;
 }
@@ -221,12 +208,12 @@ static inline void fmt_str(const char *p, kstring_t *s)
        else kputs(p, s);
 }
 
-char *bcf_fmt(bcf_t *bp, bcf1_t *b)
+char *bcf_fmt(const bcf_hdr_t *h, bcf1_t *b)
 {
        kstring_t s;
        int i, j, x;
        memset(&s, 0, sizeof(kstring_t));
-       kputs(bp->h.ns[b->tid], &s); kputc('\t', &s);
+       kputs(h->ns[b->tid], &s); kputc('\t', &s);
        kputw(b->pos + 1, &s); kputc('\t', &s);
        fmt_str(b->str, &s); kputc('\t', &s);
        fmt_str(b->ref, &s); kputc('\t', &s);
@@ -239,7 +226,7 @@ char *bcf_fmt(bcf_t *bp, bcf1_t *b)
                fmt_str(b->fmt, &s);
        }
        x = b->n_alleles * (b->n_alleles + 1) / 2;
-       for (j = 0; j < bp->h.n_smpl; ++j) {
+       for (j = 0; j < h->n_smpl; ++j) {
                kputc('\t', &s);
                for (i = 0; i < b->n_gi; ++i) {
                        if (i) kputc(':', &s);