From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 22 Oct 2009 15:41:56 +0000 (+0000)
Subject: (no commit message)
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=d410ecbf60b5aed90ee20c6ba40637ca50241edd;p=samtools.git

---

diff --git a/sam_header.c b/sam_header.c
new file mode 100644
index 0000000..b74b52b
--- /dev/null
+++ b/sam_header.c
@@ -0,0 +1,438 @@
+#include "sam_header.h"
+#include <stdio.h>
+#include <string.h>
+#include <ctype.h>
+#include <stdlib.h>
+
+const char *o_hd_tags[] = {"SO","GO",NULL};
+const char *r_hd_tags[] = {"VN",NULL};
+const char *o_sq_tags[] = {"AS","M5","UR","SP",NULL};
+const char *r_sq_tags[] = {"SN","LN",NULL};
+const char *o_rg_tags[] = {"LB","DS","PU","PI","CN","DT","PL",NULL};
+const char *r_rg_tags[] = {"ID","SM",NULL};
+const char *o_pg_tags[] = {"VN","CL",NULL};
+const char *r_pg_tags[] = {"ID",NULL};
+const char *types[]          = {"HD","SQ","RG","PG","CO",NULL};
+const char **optional_tags[] = {o_hd_tags,o_sq_tags,o_rg_tags,o_pg_tags,NULL,NULL};
+const char **required_tags[] = {r_hd_tags,r_sq_tags,r_rg_tags,r_pg_tags,NULL,NULL};
+
+
+list_t *list_append(list_t *root, void *data)
+{
+    list_t *l = root;
+    while (l && l->next)
+        l = l->next;
+    if ( l ) 
+    {
+        l->next = malloc(sizeof(list_t));
+        l = l->next;
+    }
+    else
+    {
+        l = malloc(sizeof(list_t));
+        root = l;
+    }
+    l->data = data;
+    l->next = NULL;
+    return root;
+}
+
+void list_free(list_t *root)
+{
+    list_t *l = root;
+    while (root)
+    {
+        l = root;
+        root = root->next;
+        free(l);
+    }
+}
+
+
+
+// Look for a tag "XY" in a predefined const char *[] array.
+int tag_exists(const char *tag, const char **tags)
+{
+    int itag=0;
+    if ( !tags ) return -1;
+    while ( tags[itag] )
+    {
+        if ( tags[itag][0]==tag[0] && tags[itag][1]==tag[1] ) return itag; 
+        itag++;
+    }
+    return -1;
+}
+
+
+
+// Mimics the behaviour of getline, except it returns pointer to the next chunk of the text
+//  or NULL if everything has been read. The lineptr should be freed by the caller. The
+//  newline character is stripped.
+const char *nextline(char **lineptr, size_t *n, const char *text)
+{
+    int len;
+    const char *to = text;
+
+    if ( !*to ) return NULL;
+
+    while ( *to && *to!='\n' && *to!='\r' ) to++;
+    len = to - text + 1;
+
+    if ( *to )
+    {
+        // Advance the pointer for the next call
+        if ( *to=='\n' ) to++;
+        else if ( *to=='\r' && *(to+1)=='\n' ) to+=2;
+    }
+    if ( !len )
+        return to;
+
+    if ( !*lineptr ) 
+    {
+        *lineptr = malloc(len);
+        *n = len;
+    }
+    else if ( *n<len ) 
+    {
+        *lineptr = realloc(*lineptr, len);
+        *n = len;
+    }
+    if ( !*lineptr )
+            error("FIXME\n");
+
+    memcpy(*lineptr,text,len);
+    (*lineptr)[len-1] = 0;
+
+    return to;
+}
+
+// name points to "XY", value_from points to the first character of the value string and
+//  value_to points to the last character of the value string.
+HeaderTag *new_tag(const char *name, const char *value_from, const char *value_to)
+{
+    HeaderTag *tag = malloc(sizeof(HeaderTag));
+    int len = value_to-value_from+1;
+
+    tag->key[0] = name[0];
+    tag->key[1] = name[1];
+    tag->value = malloc(len+1);
+    memcpy(tag->value,value_from,len+1);
+    tag->value[len] = 0;
+    return tag;
+}
+
+HeaderTag *header_line_has_tag(HeaderLine *hline, const char *key)
+{
+    list_t *tags = hline->tags;
+    while (tags)
+    {
+        HeaderTag *tag = tags->data;
+        if ( tag->key[0]==key[0] && tag->key[1]==key[1] ) return tag;
+        tags = tags->next;
+    }
+    return NULL;
+}
+
+#if 0
+// Is there a HeaderLine with all required fields identical to those given in the hline?
+HeaderLine *sam_header_has_line(HeaderDict *dict, HeaderLine *hline)
+{
+    HeaderLine *found=NULL;
+
+    while (dict)
+    {
+        HeaderLine *dline = dict->data;
+
+        if ( hline->type[0]!=dline->type[0] || hline->type[1]!=dline->type[1] )
+        {
+            dict = dict->next;
+            continue;
+        }
+
+        int itype = tag_exists(hline->type,types);
+        if ( itype==-1 ) error("[sam_header_has_line] Unknown type [%c%c]\n", hline->type[0],hline->type[1]);
+
+        int ireq=0, differ=0;
+        while ( required_tags[itype] && required_tags[itype][ireq] )
+        {
+            HeaderTag *t1, *t2;
+            t1 = header_line_has_tag(hline,required_tags[itype][ireq]);
+            t2 = header_line_has_tag(dline,required_tags[itype][ireq]);
+            if ( !t1 || !t2 ) error("[sam_header_has_line] Missing a required tag [%c%c]\n",
+                required_tags[itype][ireq][0],required_tags[itype][ireq][1]);
+            if ( strcmp(t1->value,t2->value) )
+            ireq++;
+        }
+        dict = dict->next; 
+    }
+    return found;
+}
+#endif
+
+HeaderLine *sam_header_line_parse(const char *headerLine)
+{
+    HeaderLine *hline;
+    HeaderTag *tag;
+    const char *from, *to;
+    from = headerLine;
+
+    if ( *from != '@' ) error("[sam_header_line_parse] expected '@', got [%s]\n", headerLine);
+    to = ++from;
+
+    while (*to && *to!='\t') to++;
+    if ( to-from != 2 ) error("[sam_header_line_parse] expected '@XY', got [%s]\n", headerLine);
+    
+    hline = malloc(sizeof(HeaderLine));
+    hline->type[0] = from[0];
+    hline->type[1] = from[1];
+    hline->tags = NULL;
+
+    int itype = tag_exists(hline->type, types);
+    
+    from = to;
+    while (*to && *to=='\t') to++;
+    if ( to-from != 1 ) 
+        error("[sam_header_line_parse] multiple tabs on line [%s] (%d)\n", headerLine,(int)(to-from));
+    from = to;
+    while (*from)
+    {
+        while (*to && *to!='\t') to++;
+
+        if ( !required_tags[itype] && !optional_tags[itype] )
+            tag = new_tag("  ",from,to-1);
+        else
+            tag = new_tag(from,from+3,to-1);
+
+        if ( header_line_has_tag(hline,tag->key) ) 
+                debug("The tag '%c%c' present (at least) twice on line [%s]\n", tag->key[0],tag->key[1], headerLine);
+        hline->tags = list_append(hline->tags, tag);
+
+        from = to;
+        while (*to && *to=='\t') to++;
+        if ( *to && to-from != 1 ) 
+                error("[sam_header_line_parse] multiple tabs on line [%s] (%d)\n", headerLine,(int)(to-from));
+
+        from = to;
+    }
+    return hline;
+}
+
+
+// Must be of an existing type, all tags must be recognised and all required tags must be present
+int sam_header_line_validate(HeaderLine *hline)
+{
+    list_t *tags;
+    HeaderTag *tag;
+    int itype, itag;
+    
+    // Is the type correct?
+    itype = tag_exists(hline->type, types);
+    if ( itype==-1 ) 
+    {
+        debug("The type [%c%c] not recognised.\n", hline->type[0],hline->type[1]);
+        return 0;
+    }
+
+    // Has all required tags?
+    itag = 0;
+    while ( required_tags[itype] && required_tags[itype][itag] )
+    {
+        if ( !header_line_has_tag(hline,required_tags[itype][itag]) )
+        {
+            debug("The tag [%c%c] required for [%c%c] not present.\n", required_tags[itype][itag][0],required_tags[itype][itag][1],
+                hline->type[0],hline->type[1]);
+            return 0;
+        }
+        itag++;
+    }
+
+    // Are all tags recognised?
+    tags = hline->tags;
+    while ( tags )
+    {
+        tag = tags->data;
+        if ( !tag_exists(tag->key,required_tags[itype]) && !tag_exists(tag->key,optional_tags[itype]) )
+        {
+            debug("Unknown tag [%c%c] for [%c%c].\n", tag->key[0],tag->key[1], hline->type[0],hline->type[1]);
+            return 0;
+        }
+        tags = tags->next;
+    }
+
+    return 1;
+}
+
+void print_header_line(HeaderLine *hline)
+{
+    list_t *tags = hline->tags;
+    HeaderTag *tag;
+
+    printf("@%c%c", hline->type[0],hline->type[1]);
+    while (tags)
+    {
+        tag = tags->data;
+        printf("\t%c%c:%s", tag->key[0],tag->key[1],tag->value);
+        tags = tags->next;
+    }
+    printf("\n");
+}
+
+
+void sam_header_free(HeaderDict *header)
+{
+    list_t *hlines = header;
+    while (hlines)
+    {
+        HeaderLine *hline = hlines->data;
+        list_t *tags = hline->tags;
+        while (tags)
+        {
+            HeaderTag *tag = tags->data;
+            free(tag->value);
+            free(tag);
+            tags = tags->next;
+        }
+        list_free(hline->tags);
+        free(hline);
+        hlines = hlines->next;
+    }
+    list_free(header);
+}
+
+// Returns a newly allocated string
+char *sam_header_write(const HeaderDict *header)
+{
+    char *out = NULL;
+    int len=0, nout=0;
+    const list_t *hlines;
+
+    // Calculate the length of the string to allocate
+    hlines = header;
+    while (hlines)
+    {
+        len += 4;   // @XY and \n
+
+        HeaderLine *hline = hlines->data;
+        list_t *tags = hline->tags;
+        while (tags)
+        {
+            HeaderTag *tag = tags->data;
+            len += strlen(tag->value) + 1;                  // \t
+            if ( tag->key[0]!=' ' || tag->key[1]!=' ' )
+                len += strlen(tag->value) + 3;              // XY:
+            tags = tags->next;
+        }
+        hlines = hlines->next;
+    }
+
+    nout = 0;
+    out  = malloc(len+1);
+    hlines = header;
+    while (hlines)
+    {
+        HeaderLine *hline = hlines->data;
+
+        nout += sprintf(out+nout,"@%c%c",hline->type[0],hline->type[1]);
+
+        list_t *tags = hline->tags;
+        while (tags)
+        {
+            HeaderTag *tag = tags->data;
+            nout += sprintf(out+nout,"\t");
+            if ( tag->key[0]!=' ' || tag->key[1]!=' ' )
+                nout += sprintf(out+nout,"%c%c:", tag->key[0],tag->key[1]);
+            nout += sprintf(out+nout,"%s", tag->value);
+            tags = tags->next;
+        }
+        hlines = hlines->next;
+        nout += sprintf(out+nout,"\n");
+    }
+    out[len] = 0;
+    return out;
+}
+
+HeaderDict *sam_header_parse(const char *headerText)
+{
+    list_t *hlines = NULL;
+    HeaderLine *hline;
+    const char *text;
+    char *buf=NULL;
+    size_t nbuf = 0;
+
+    if ( !headerText )
+        error("FIXME");
+
+    text = headerText;
+    while ( (text=nextline(&buf, &nbuf, text)) )
+    {
+        hline = sam_header_line_parse(buf);
+        if ( sam_header_line_validate(hline) )
+            hlines = list_append(hlines, hline);
+        else
+        {
+            sam_header_free(hlines);
+            return NULL;
+        }
+    }
+    if ( buf ) free(buf);
+
+    return hlines;
+}
+
+khash_t(str) *sam_header_lookup_table(const HeaderDict *dict, char type[2], char key_tag[2], char value_tag[2])
+{
+    const list_t *l   = dict;
+    khash_t(str) *tbl = kh_init(str);
+    khiter_t k;
+    int ret;
+
+    while (l)
+    {
+        HeaderLine *hline = l->data;
+        if ( hline->type[0]!=type[0] || hline->type[1]!=type[1] ) 
+        {
+            l = l->next;
+            continue;
+        }
+        
+        HeaderTag *key, *value;
+        key   = header_line_has_tag(hline,key_tag);
+        value = header_line_has_tag(hline,value_tag); 
+        if ( !key || !value )
+        {
+            l = l->next;
+            continue;
+        }
+        
+        k = kh_get(str, tbl, key->value);
+        if ( k != kh_end(tbl) )
+            debug("[sam_header_lookup_table] They key %s not unique.\n", key->value);
+        k = kh_put(str, tbl, key->value, &ret);
+        kh_value(tbl, k) = value->value;
+
+        l = l->next;
+    }
+    return tbl;
+}
+
+
+#if 0
+TODO
+HeaderDict *sam_header_merge(int n, const HeaderDict **dicts)
+{
+    HeaderDict *out=NULL;
+    int idict;
+
+    for (idict=0; idict<n; idict++)
+    {
+        list_t *hlines = dicts[idict];
+        while (hlines)
+        {
+            HeaderLine *hline = sam_header_has_line(out, hlines->data);
+            sam_header_line_merge(hline,hlines->data);
+            hlines = hlines->next;
+        }
+    }
+}
+#endif
+
diff --git a/sam_header.h b/sam_header.h
new file mode 100644
index 0000000..4f633ed
--- /dev/null
+++ b/sam_header.h
@@ -0,0 +1,48 @@
+#ifndef __SAM_HEADER_H__
+#define __SAM_HEADER_H__
+
+#include "khash.h"
+KHASH_MAP_INIT_STR(str,const char *)
+
+// HeaderDict is a list_t of header lines. Each HeaderLine holds a list of tags.
+struct _list_t
+{
+    struct _list_t *next;
+    void *data;
+};
+typedef struct _list_t list_t;
+typedef list_t HeaderDict;
+
+typedef struct
+{
+    char key[2];
+    char *value;
+}
+HeaderTag;
+
+typedef struct
+{
+    char type[2];
+    list_t *tags;
+}
+HeaderLine;
+
+
+void debug(const char *format, ...);
+void error(const char *format, ...);
+
+HeaderDict *sam_header_parse(const char *headerText);
+void sam_header_free(HeaderDict *header);
+char *sam_header_write(const HeaderDict *headerDict);   // returns a newly allocated string
+
+khash_t(str) *sam_header_lookup_table(const HeaderDict *dict, char type[2], char key_tag[2], char value_tag[2]);
+
+list_t *list_append(list_t *root, void *data);
+void list_free(list_t *root);
+
+//HeaderDict *sam_header_merge(int n, const HeaderDict **dicts);  // if n=1, the func clones the dictionary
+//char *sam_header_get(const HeaderDict *d, char type[2], int i, char tag[2]);  
+//int sam_header_ins(HeaderDict *d, char tp[2], int i, char tg[2], const char *s);  
+//int sam_header_del(HeaderDict *d, char type[2], int i, char tag[2]);  
+
+#endif