--- /dev/null
+#include "sam_header.h"
+#include <stdio.h>
+#include <string.h>
+#include <ctype.h>
+#include <stdlib.h>
+#include <stdarg.h>
+
+#include "khash.h"
+KHASH_MAP_INIT_STR(str, const char *)
+
+struct _HeaderList
+{
+ struct _HeaderList *next;
+ void *data;
+};
+typedef struct _HeaderList list_t;
+typedef list_t HeaderDict;
+
+typedef struct
+{
+ char key[2];
+ char *value;
+}
+HeaderTag;
+
+typedef struct
+{
+ char type[2];
+ list_t *tags;
+}
+HeaderLine;
+
+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 *u_sq_tags[] = {"SN",NULL};
+
+const char *o_rg_tags[] = {"LB","DS","PU","PI","CN","DT","PL",NULL};
+const char *r_rg_tags[] = {"ID",NULL};
+const char *u_rg_tags[] = {"ID",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};
+const char **unique_tags[] = {NULL, u_sq_tags,u_rg_tags,NULL,NULL,NULL};
+
+
+static void debug(const char *format, ...)
+{
+ va_list ap;
+ va_start(ap, format);
+ vfprintf(stderr, format, ap);
+ va_end(ap);
+}
+
+static 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;
+}
+
+static 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.
+static 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.
+static 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 ) {
+ debug("[nextline] Insufficient memory!\n");
+ return 0;
+ }
+
+ 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.
+static 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;
+}
+
+static 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;
+}
+
+
+// Return codes:
+// 0 .. different types or unique tags differ or conflicting tags, cannot be merged
+// 1 .. all tags identical -> no need to merge, drop one
+// 2 .. the unique tags match and there are some conflicting tags (same tag, different value) -> error, cannot be merged nor duplicated
+// 3 .. there are some missing complementary tags and no unique conflict -> can be merged into a single line
+static int sam_header_compare_lines(HeaderLine *hline1, HeaderLine *hline2)
+{
+ HeaderTag *t1, *t2;
+
+ if ( hline1->type[0]!=hline2->type[0] || hline1->type[1]!=hline2->type[1] )
+ return 0;
+
+ int itype = tag_exists(hline1->type,types);
+ if ( itype==-1 ) {
+ debug("[sam_header_compare_lines] Unknown type [%c%c]\n", hline1->type[0],hline1->type[1]);
+ return -1; // FIXME (lh3): error; I do not know how this will be handled in Petr's code
+ }
+
+ if ( unique_tags[itype] )
+ {
+ t1 = header_line_has_tag(hline1,unique_tags[itype][0]);
+ t2 = header_line_has_tag(hline2,unique_tags[itype][0]);
+ if ( !t1 || !t2 ) // this should never happen, the unique tags are required
+ return 2;
+
+ if ( strcmp(t1->value,t2->value) )
+ return 0; // the unique tags differ, cannot be merged
+ }
+ if ( !required_tags[itype] && !optional_tags[itype] )
+ {
+ t1 = hline1->tags->data;
+ t2 = hline2->tags->data;
+ if ( !strcmp(t1->value,t2->value) ) return 1; // identical comments
+ return 0;
+ }
+
+ int missing=0, itag=0;
+ while ( required_tags[itype] && required_tags[itype][itag] )
+ {
+ t1 = header_line_has_tag(hline1,required_tags[itype][itag]);
+ t2 = header_line_has_tag(hline2,required_tags[itype][itag]);
+ if ( !t1 && !t2 )
+ return 2; // this should never happen
+ else if ( !t1 || !t2 )
+ missing = 1; // there is some tag missing in one of the hlines
+ else if ( strcmp(t1->value,t2->value) )
+ {
+ if ( unique_tags[itype] )
+ return 2; // the lines have a matching unique tag but have a conflicting tag
+
+ return 0; // the lines contain conflicting tags, cannot be merged
+ }
+ itag++;
+ }
+ itag = 0;
+ while ( optional_tags[itype] && optional_tags[itype][itag] )
+ {
+ t1 = header_line_has_tag(hline1,optional_tags[itype][itag]);
+ t2 = header_line_has_tag(hline2,optional_tags[itype][itag]);
+ if ( !t1 && !t2 )
+ {
+ itag++;
+ continue;
+ }
+ if ( !t1 || !t2 )
+ missing = 1; // there is some tag missing in one of the hlines
+ else if ( strcmp(t1->value,t2->value) )
+ {
+ if ( unique_tags[itype] )
+ return 2; // the lines have a matching unique tag but have a conflicting tag
+
+ return 0; // the lines contain conflicting tags, cannot be merged
+ }
+ itag++;
+ }
+ if ( missing ) return 3; // there are some missing complementary tags with no conflicts, can be merged
+ return 1;
+}
+
+
+static HeaderLine *sam_header_line_clone(const HeaderLine *hline)
+{
+ list_t *tags;
+ HeaderLine *out = malloc(sizeof(HeaderLine));
+ out->type[0] = hline->type[0];
+ out->type[1] = hline->type[1];
+ out->tags = NULL;
+
+ tags = hline->tags;
+ while (tags)
+ {
+ HeaderTag *old = tags->data;
+
+ HeaderTag *new = malloc(sizeof(HeaderTag));
+ new->key[0] = old->key[0];
+ new->key[1] = old->key[1];
+ new->value = strdup(old->value);
+ out->tags = list_append(out->tags, new);
+
+ tags = tags->next;
+ }
+ return out;
+}
+
+static int sam_header_line_merge_with(HeaderLine *out_hline, const HeaderLine *tmpl_hline)
+{
+ list_t *tmpl_tags;
+
+ if ( out_hline->type[0]!=tmpl_hline->type[0] || out_hline->type[1]!=tmpl_hline->type[1] )
+ return 0;
+
+ tmpl_tags = tmpl_hline->tags;
+ while (tmpl_tags)
+ {
+ HeaderTag *tmpl_tag = tmpl_tags->data;
+ HeaderTag *out_tag = header_line_has_tag(out_hline, tmpl_tag->key);
+ if ( !out_tag )
+ {
+ HeaderTag *tag = malloc(sizeof(HeaderTag));
+ tag->key[0] = tmpl_tag->key[0];
+ tag->key[1] = tmpl_tag->key[1];
+ tag->value = strdup(tmpl_tag->value);
+ out_hline->tags = list_append(out_hline->tags,tag);
+ }
+ tmpl_tags = tmpl_tags->next;
+ }
+ return 1;
+}
+
+
+static HeaderLine *sam_header_line_parse(const char *headerLine)
+{
+ HeaderLine *hline;
+ HeaderTag *tag;
+ const char *from, *to;
+ from = headerLine;
+
+ if ( *from != '@' ) {
+ debug("[sam_header_line_parse] expected '@', got [%s]\n", headerLine);
+ return 0;
+ }
+ to = ++from;
+
+ while (*to && *to!='\t') to++;
+ if ( to-from != 2 ) {
+ debug("[sam_header_line_parse] expected '@XY', got [%s]\n", headerLine);
+ return 0;
+ }
+
+ 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 ) {
+ debug("[sam_header_line_parse] multiple tabs on line [%s] (%d)\n", headerLine,(int)(to-from));
+ return 0;
+ }
+ 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 ) {
+ debug("[sam_header_line_parse] multiple tabs on line [%s] (%d)\n", headerLine,(int)(to-from));
+ return 0;
+ }
+
+ from = to;
+ }
+ return hline;
+}
+
+
+// Must be of an existing type, all tags must be recognised and all required tags must be present
+static 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;
+}
+
+
+static void print_header_line(FILE *fp, HeaderLine *hline)
+{
+ list_t *tags = hline->tags;
+ HeaderTag *tag;
+
+ fprintf(fp, "@%c%c", hline->type[0],hline->type[1]);
+ while (tags)
+ {
+ tag = tags->data;
+
+ fprintf(fp, "\t");
+ if ( tag->key[0]!=' ' || tag->key[1]!=' ' )
+ fprintf(fp, "%c%c:", tag->key[0],tag->key[1]);
+ fprintf(fp, "%s", tag->value);
+
+ tags = tags->next;
+ }
+ fprintf(fp,"\n");
+}
+
+
+static void sam_header_line_free(HeaderLine *hline)
+{
+ 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);
+}
+
+void sam_header_free(void *_header)
+{
+ HeaderDict *header = (HeaderDict*)_header;
+ list_t *hlines = header;
+ while (hlines)
+ {
+ sam_header_line_free(hlines->data);
+ hlines = hlines->next;
+ }
+ list_free(header);
+}
+
+HeaderDict *sam_header_clone(const HeaderDict *dict)
+{
+ HeaderDict *out = NULL;
+ while (dict)
+ {
+ HeaderLine *hline = dict->data;
+ out = list_append(out, sam_header_line_clone(hline));
+ dict = dict->next;
+ }
+ return out;
+}
+
+// Returns a newly allocated string
+char *sam_header_write(const void *_header)
+{
+ const HeaderDict *header = (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;
+}
+
+void *sam_header_parse2(const char *headerText)
+{
+ list_t *hlines = NULL;
+ HeaderLine *hline;
+ const char *text;
+ char *buf=NULL;
+ size_t nbuf = 0;
+
+ if ( !headerText )
+ return 0;
+
+ text = headerText;
+ while ( (text=nextline(&buf, &nbuf, text)) )
+ {
+ hline = sam_header_line_parse(buf);
+ if ( hline && sam_header_line_validate(hline) )
+ hlines = list_append(hlines, hline);
+ else
+ {
+ if (hline) sam_header_line_free(hline);
+ sam_header_free(hlines);
+ if ( buf ) free(buf);
+ return NULL;
+ }
+ }
+ if ( buf ) free(buf);
+
+ return hlines;
+}
+
+void *sam_header2tbl(const void *_dict, char type[2], char key_tag[2], char value_tag[2])
+{
+ const HeaderDict *dict = (const HeaderDict*)_dict;
+ const list_t *l = dict;
+ khash_t(str) *tbl = kh_init(str);
+ khiter_t k;
+ int ret;
+
+ if (_dict == 0) return tbl; // return an empty (not null) hash table
+ 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;
+}
+
+char **sam_header2list(const void *_dict, char type[2], char key_tag[2], int *_n)
+{
+ const HeaderDict *dict = (const HeaderDict*)_dict;
+ const list_t *l = dict;
+ int max, n;
+ char **ret;
+
+ ret = 0; *_n = max = n = 0;
+ while (l)
+ {
+ HeaderLine *hline = l->data;
+ if ( hline->type[0]!=type[0] || hline->type[1]!=type[1] )
+ {
+ l = l->next;
+ continue;
+ }
+
+ HeaderTag *key;
+ key = header_line_has_tag(hline,key_tag);
+ if ( !key )
+ {
+ l = l->next;
+ continue;
+ }
+
+ if (n == max) {
+ max = max? max<<1 : 4;
+ ret = realloc(ret, max * sizeof(void*));
+ }
+ ret[n++] = key->value;
+
+ l = l->next;
+ }
+ *_n = n;
+ return ret;
+}
+
+const char *sam_tbl_get(void *h, const char *key)
+{
+ khash_t(str) *tbl = (khash_t(str)*)h;
+ khint_t k;
+ k = kh_get(str, tbl, key);
+ return k == kh_end(tbl)? 0 : kh_val(tbl, k);
+}
+
+int sam_tbl_size(void *h)
+{
+ khash_t(str) *tbl = (khash_t(str)*)h;
+ return h? kh_size(tbl) : 0;
+}
+
+void sam_tbl_destroy(void *h)
+{
+ khash_t(str) *tbl = (khash_t(str)*)h;
+ kh_destroy(str, tbl);
+}
+
+void *sam_header_merge(int n, const void **_dicts)
+{
+ const HeaderDict **dicts = (const HeaderDict**)_dicts;
+ HeaderDict *out_dict;
+ int idict, status;
+
+ if ( n<2 ) return NULL;
+
+ out_dict = sam_header_clone(dicts[0]);
+
+ for (idict=1; idict<n; idict++)
+ {
+ const list_t *tmpl_hlines = dicts[idict];
+
+ while ( tmpl_hlines )
+ {
+ list_t *out_hlines = out_dict;
+ int inserted = 0;
+ while ( out_hlines )
+ {
+ status = sam_header_compare_lines(tmpl_hlines->data, out_hlines->data);
+ if ( status==0 )
+ {
+ out_hlines = out_hlines->next;
+ continue;
+ }
+
+ if ( status==2 )
+ {
+ print_header_line(stderr,tmpl_hlines->data);
+ print_header_line(stderr,out_hlines->data);
+ debug("Conflicting lines, cannot merge the headers.\n");
+ return 0;
+ }
+ if ( status==3 )
+ sam_header_line_merge_with(out_hlines->data, tmpl_hlines->data);
+
+ inserted = 1;
+ break;
+ }
+ if ( !inserted )
+ out_dict = list_append(out_dict, sam_header_line_clone(tmpl_hlines->data));
+
+ tmpl_hlines = tmpl_hlines->next;
+ }
+ }
+
+ return out_dict;
+}
+
+
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