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comparison PsiCLASS-1.0.2/samtools-0.1.19/sam_header.c @ 0:903fc43d6227 draft default tip

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author lsong10
date Fri, 26 Mar 2021 16:52:45 +0000
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1 #include "sam_header.h"
2 #include <stdio.h>
3 #include <string.h>
4 #include <ctype.h>
5 #include <stdlib.h>
6 #include <stdarg.h>
7
8 #include "khash.h"
9 KHASH_MAP_INIT_STR(str, const char *)
10
11 struct _HeaderList
12 {
13 struct _HeaderList *last; // Hack: Used and maintained only by list_append_to_end. Maintained in the root node only.
14 struct _HeaderList *next;
15 void *data;
16 };
17 typedef struct _HeaderList list_t;
18 typedef list_t HeaderDict;
19
20 typedef struct
21 {
22 char key[2];
23 char *value;
24 }
25 HeaderTag;
26
27 typedef struct
28 {
29 char type[2];
30 list_t *tags;
31 }
32 HeaderLine;
33
34 const char *o_hd_tags[] = {"SO","GO",NULL};
35 const char *r_hd_tags[] = {"VN",NULL};
36
37 const char *o_sq_tags[] = {"AS","M5","UR","SP",NULL};
38 const char *r_sq_tags[] = {"SN","LN",NULL};
39 const char *u_sq_tags[] = {"SN",NULL};
40
41 const char *o_rg_tags[] = {"CN","DS","DT","FO","KS","LB","PG","PI","PL","PU","SM",NULL};
42 const char *r_rg_tags[] = {"ID",NULL};
43 const char *u_rg_tags[] = {"ID",NULL};
44
45 const char *o_pg_tags[] = {"VN","CL",NULL};
46 const char *r_pg_tags[] = {"ID",NULL};
47
48 const char *types[] = {"HD","SQ","RG","PG","CO",NULL};
49 const char **optional_tags[] = {o_hd_tags,o_sq_tags,o_rg_tags,o_pg_tags,NULL,NULL};
50 const char **required_tags[] = {r_hd_tags,r_sq_tags,r_rg_tags,r_pg_tags,NULL,NULL};
51 const char **unique_tags[] = {NULL, u_sq_tags,u_rg_tags,NULL,NULL,NULL};
52
53
54 static void debug(const char *format, ...)
55 {
56 va_list ap;
57 va_start(ap, format);
58 vfprintf(stderr, format, ap);
59 va_end(ap);
60 }
61
62 #if 0
63 // Replaced by list_append_to_end
64 static list_t *list_prepend(list_t *root, void *data)
65 {
66 list_t *l = malloc(sizeof(list_t));
67 l->next = root;
68 l->data = data;
69 return l;
70 }
71 #endif
72
73 // Relies on the root->last being correct. Do not use with the other list_*
74 // routines unless they are fixed to modify root->last as well.
75 static list_t *list_append_to_end(list_t *root, void *data)
76 {
77 list_t *l = malloc(sizeof(list_t));
78 l->last = l;
79 l->next = NULL;
80 l->data = data;
81
82 if ( !root )
83 return l;
84
85 root->last->next = l;
86 root->last = l;
87 return root;
88 }
89
90 static list_t *list_append(list_t *root, void *data)
91 {
92 list_t *l = root;
93 while (l && l->next)
94 l = l->next;
95 if ( l )
96 {
97 l->next = malloc(sizeof(list_t));
98 l = l->next;
99 }
100 else
101 {
102 l = malloc(sizeof(list_t));
103 root = l;
104 }
105 l->data = data;
106 l->next = NULL;
107 return root;
108 }
109
110 static void list_free(list_t *root)
111 {
112 list_t *l = root;
113 while (root)
114 {
115 l = root;
116 root = root->next;
117 free(l);
118 }
119 }
120
121
122
123 // Look for a tag "XY" in a predefined const char *[] array.
124 static int tag_exists(const char *tag, const char **tags)
125 {
126 int itag=0;
127 if ( !tags ) return -1;
128 while ( tags[itag] )
129 {
130 if ( tags[itag][0]==tag[0] && tags[itag][1]==tag[1] ) return itag;
131 itag++;
132 }
133 return -1;
134 }
135
136
137
138 // Mimics the behaviour of getline, except it returns pointer to the next chunk of the text
139 // or NULL if everything has been read. The lineptr should be freed by the caller. The
140 // newline character is stripped.
141 static const char *nextline(char **lineptr, size_t *n, const char *text)
142 {
143 int len;
144 const char *to = text;
145
146 if ( !*to ) return NULL;
147
148 while ( *to && *to!='\n' && *to!='\r' ) to++;
149 len = to - text + 1;
150
151 if ( *to )
152 {
153 // Advance the pointer for the next call
154 if ( *to=='\n' ) to++;
155 else if ( *to=='\r' && *(to+1)=='\n' ) to+=2;
156 }
157 if ( !len )
158 return to;
159
160 if ( !*lineptr )
161 {
162 *lineptr = malloc(len);
163 *n = len;
164 }
165 else if ( *n<len )
166 {
167 *lineptr = realloc(*lineptr, len);
168 *n = len;
169 }
170 if ( !*lineptr ) {
171 debug("[nextline] Insufficient memory!\n");
172 return 0;
173 }
174
175 memcpy(*lineptr,text,len);
176 (*lineptr)[len-1] = 0;
177
178 return to;
179 }
180
181 // name points to "XY", value_from points to the first character of the value string and
182 // value_to points to the last character of the value string.
183 static HeaderTag *new_tag(const char *name, const char *value_from, const char *value_to)
184 {
185 HeaderTag *tag = malloc(sizeof(HeaderTag));
186 int len = value_to-value_from+1;
187
188 tag->key[0] = name[0];
189 tag->key[1] = name[1];
190 tag->value = malloc(len+1);
191 memcpy(tag->value,value_from,len+1);
192 tag->value[len] = 0;
193 return tag;
194 }
195
196 static HeaderTag *header_line_has_tag(HeaderLine *hline, const char *key)
197 {
198 list_t *tags = hline->tags;
199 while (tags)
200 {
201 HeaderTag *tag = tags->data;
202 if ( tag->key[0]==key[0] && tag->key[1]==key[1] ) return tag;
203 tags = tags->next;
204 }
205 return NULL;
206 }
207
208
209 // Return codes:
210 // 0 .. different types or unique tags differ or conflicting tags, cannot be merged
211 // 1 .. all tags identical -> no need to merge, drop one
212 // 2 .. the unique tags match and there are some conflicting tags (same tag, different value) -> error, cannot be merged nor duplicated
213 // 3 .. there are some missing complementary tags and no unique conflict -> can be merged into a single line
214 static int sam_header_compare_lines(HeaderLine *hline1, HeaderLine *hline2)
215 {
216 HeaderTag *t1, *t2;
217
218 if ( hline1->type[0]!=hline2->type[0] || hline1->type[1]!=hline2->type[1] )
219 return 0;
220
221 int itype = tag_exists(hline1->type,types);
222 if ( itype==-1 ) {
223 debug("[sam_header_compare_lines] Unknown type [%c%c]\n", hline1->type[0],hline1->type[1]);
224 return -1; // FIXME (lh3): error; I do not know how this will be handled in Petr's code
225 }
226
227 if ( unique_tags[itype] )
228 {
229 t1 = header_line_has_tag(hline1,unique_tags[itype][0]);
230 t2 = header_line_has_tag(hline2,unique_tags[itype][0]);
231 if ( !t1 || !t2 ) // this should never happen, the unique tags are required
232 return 2;
233
234 if ( strcmp(t1->value,t2->value) )
235 return 0; // the unique tags differ, cannot be merged
236 }
237 if ( !required_tags[itype] && !optional_tags[itype] )
238 {
239 t1 = hline1->tags->data;
240 t2 = hline2->tags->data;
241 if ( !strcmp(t1->value,t2->value) ) return 1; // identical comments
242 return 0;
243 }
244
245 int missing=0, itag=0;
246 while ( required_tags[itype] && required_tags[itype][itag] )
247 {
248 t1 = header_line_has_tag(hline1,required_tags[itype][itag]);
249 t2 = header_line_has_tag(hline2,required_tags[itype][itag]);
250 if ( !t1 && !t2 )
251 return 2; // this should never happen
252 else if ( !t1 || !t2 )
253 missing = 1; // there is some tag missing in one of the hlines
254 else if ( strcmp(t1->value,t2->value) )
255 {
256 if ( unique_tags[itype] )
257 return 2; // the lines have a matching unique tag but have a conflicting tag
258
259 return 0; // the lines contain conflicting tags, cannot be merged
260 }
261 itag++;
262 }
263 itag = 0;
264 while ( optional_tags[itype] && optional_tags[itype][itag] )
265 {
266 t1 = header_line_has_tag(hline1,optional_tags[itype][itag]);
267 t2 = header_line_has_tag(hline2,optional_tags[itype][itag]);
268 if ( !t1 && !t2 )
269 {
270 itag++;
271 continue;
272 }
273 if ( !t1 || !t2 )
274 missing = 1; // there is some tag missing in one of the hlines
275 else if ( strcmp(t1->value,t2->value) )
276 {
277 if ( unique_tags[itype] )
278 return 2; // the lines have a matching unique tag but have a conflicting tag
279
280 return 0; // the lines contain conflicting tags, cannot be merged
281 }
282 itag++;
283 }
284 if ( missing ) return 3; // there are some missing complementary tags with no conflicts, can be merged
285 return 1;
286 }
287
288
289 static HeaderLine *sam_header_line_clone(const HeaderLine *hline)
290 {
291 list_t *tags;
292 HeaderLine *out = malloc(sizeof(HeaderLine));
293 out->type[0] = hline->type[0];
294 out->type[1] = hline->type[1];
295 out->tags = NULL;
296
297 tags = hline->tags;
298 while (tags)
299 {
300 HeaderTag *old = tags->data;
301
302 HeaderTag *new = malloc(sizeof(HeaderTag));
303 new->key[0] = old->key[0];
304 new->key[1] = old->key[1];
305 new->value = strdup(old->value);
306 out->tags = list_append(out->tags, new);
307
308 tags = tags->next;
309 }
310 return out;
311 }
312
313 static int sam_header_line_merge_with(HeaderLine *out_hline, const HeaderLine *tmpl_hline)
314 {
315 list_t *tmpl_tags;
316
317 if ( out_hline->type[0]!=tmpl_hline->type[0] || out_hline->type[1]!=tmpl_hline->type[1] )
318 return 0;
319
320 tmpl_tags = tmpl_hline->tags;
321 while (tmpl_tags)
322 {
323 HeaderTag *tmpl_tag = tmpl_tags->data;
324 HeaderTag *out_tag = header_line_has_tag(out_hline, tmpl_tag->key);
325 if ( !out_tag )
326 {
327 HeaderTag *tag = malloc(sizeof(HeaderTag));
328 tag->key[0] = tmpl_tag->key[0];
329 tag->key[1] = tmpl_tag->key[1];
330 tag->value = strdup(tmpl_tag->value);
331 out_hline->tags = list_append(out_hline->tags,tag);
332 }
333 tmpl_tags = tmpl_tags->next;
334 }
335 return 1;
336 }
337
338
339 static HeaderLine *sam_header_line_parse(const char *headerLine)
340 {
341 HeaderLine *hline;
342 HeaderTag *tag;
343 const char *from, *to;
344 from = headerLine;
345
346 if ( *from != '@' ) {
347 debug("[sam_header_line_parse] expected '@', got [%s]\n", headerLine);
348 return 0;
349 }
350 to = ++from;
351
352 while (*to && *to!='\t') to++;
353 if ( to-from != 2 ) {
354 debug("[sam_header_line_parse] expected '@XY', got [%s]\nHint: The header tags must be tab-separated.\n", headerLine);
355 return 0;
356 }
357
358 hline = malloc(sizeof(HeaderLine));
359 hline->type[0] = from[0];
360 hline->type[1] = from[1];
361 hline->tags = NULL;
362
363 int itype = tag_exists(hline->type, types);
364
365 from = to;
366 while (*to && *to=='\t') to++;
367 if ( to-from != 1 ) {
368 debug("[sam_header_line_parse] multiple tabs on line [%s] (%d)\n", headerLine,(int)(to-from));
369 free(hline);
370 return 0;
371 }
372 from = to;
373 while (*from)
374 {
375 while (*to && *to!='\t') to++;
376
377 if ( !required_tags[itype] && !optional_tags[itype] )
378 {
379 // CO is a special case, it can contain anything, including tabs
380 if ( *to ) { to++; continue; }
381 tag = new_tag(" ",from,to-1);
382 }
383 else
384 tag = new_tag(from,from+3,to-1);
385
386 if ( header_line_has_tag(hline,tag->key) )
387 debug("The tag '%c%c' present (at least) twice on line [%s]\n", tag->key[0],tag->key[1], headerLine);
388 hline->tags = list_append(hline->tags, tag);
389
390 from = to;
391 while (*to && *to=='\t') to++;
392 if ( *to && to-from != 1 ) {
393 debug("[sam_header_line_parse] multiple tabs on line [%s] (%d)\n", headerLine,(int)(to-from));
394 return 0;
395 }
396
397 from = to;
398 }
399 return hline;
400 }
401
402
403 // Must be of an existing type, all tags must be recognised and all required tags must be present
404 static int sam_header_line_validate(HeaderLine *hline)
405 {
406 list_t *tags;
407 HeaderTag *tag;
408 int itype, itag;
409
410 // Is the type correct?
411 itype = tag_exists(hline->type, types);
412 if ( itype==-1 )
413 {
414 debug("The type [%c%c] not recognised.\n", hline->type[0],hline->type[1]);
415 return 0;
416 }
417
418 // Has all required tags?
419 itag = 0;
420 while ( required_tags[itype] && required_tags[itype][itag] )
421 {
422 if ( !header_line_has_tag(hline,required_tags[itype][itag]) )
423 {
424 debug("The tag [%c%c] required for [%c%c] not present.\n", required_tags[itype][itag][0],required_tags[itype][itag][1],
425 hline->type[0],hline->type[1]);
426 return 0;
427 }
428 itag++;
429 }
430
431 // Are all tags recognised?
432 tags = hline->tags;
433 while ( tags )
434 {
435 tag = tags->data;
436 if ( !tag_exists(tag->key,required_tags[itype]) && !tag_exists(tag->key,optional_tags[itype]) )
437 {
438 // Lower case tags are user-defined values.
439 if( !(islower(tag->key[0]) || islower(tag->key[1])) )
440 {
441 // Neither is lower case, but tag was not recognized.
442 debug("Unknown tag [%c%c] for [%c%c].\n", tag->key[0],tag->key[1], hline->type[0],hline->type[1]);
443 // return 0; // Even unknown tags are allowed - for forward compatibility with new attributes
444 }
445 // else - allow user defined tag
446 }
447 tags = tags->next;
448 }
449
450 return 1;
451 }
452
453
454 static void print_header_line(FILE *fp, HeaderLine *hline)
455 {
456 list_t *tags = hline->tags;
457 HeaderTag *tag;
458
459 fprintf(fp, "@%c%c", hline->type[0],hline->type[1]);
460 while (tags)
461 {
462 tag = tags->data;
463
464 fprintf(fp, "\t");
465 if ( tag->key[0]!=' ' || tag->key[1]!=' ' )
466 fprintf(fp, "%c%c:", tag->key[0],tag->key[1]);
467 fprintf(fp, "%s", tag->value);
468
469 tags = tags->next;
470 }
471 fprintf(fp,"\n");
472 }
473
474
475 static void sam_header_line_free(HeaderLine *hline)
476 {
477 list_t *tags = hline->tags;
478 while (tags)
479 {
480 HeaderTag *tag = tags->data;
481 free(tag->value);
482 free(tag);
483 tags = tags->next;
484 }
485 list_free(hline->tags);
486 free(hline);
487 }
488
489 void sam_header_free(void *_header)
490 {
491 HeaderDict *header = (HeaderDict*)_header;
492 list_t *hlines = header;
493 while (hlines)
494 {
495 sam_header_line_free(hlines->data);
496 hlines = hlines->next;
497 }
498 list_free(header);
499 }
500
501 HeaderDict *sam_header_clone(const HeaderDict *dict)
502 {
503 HeaderDict *out = NULL;
504 while (dict)
505 {
506 HeaderLine *hline = dict->data;
507 out = list_append(out, sam_header_line_clone(hline));
508 dict = dict->next;
509 }
510 return out;
511 }
512
513 // Returns a newly allocated string
514 char *sam_header_write(const void *_header)
515 {
516 const HeaderDict *header = (const HeaderDict*)_header;
517 char *out = NULL;
518 int len=0, nout=0;
519 const list_t *hlines;
520
521 // Calculate the length of the string to allocate
522 hlines = header;
523 while (hlines)
524 {
525 len += 4; // @XY and \n
526
527 HeaderLine *hline = hlines->data;
528 list_t *tags = hline->tags;
529 while (tags)
530 {
531 HeaderTag *tag = tags->data;
532 len += strlen(tag->value) + 1; // \t
533 if ( tag->key[0]!=' ' || tag->key[1]!=' ' )
534 len += strlen(tag->value) + 3; // XY:
535 tags = tags->next;
536 }
537 hlines = hlines->next;
538 }
539
540 nout = 0;
541 out = malloc(len+1);
542 hlines = header;
543 while (hlines)
544 {
545 HeaderLine *hline = hlines->data;
546
547 nout += sprintf(out+nout,"@%c%c",hline->type[0],hline->type[1]);
548
549 list_t *tags = hline->tags;
550 while (tags)
551 {
552 HeaderTag *tag = tags->data;
553 nout += sprintf(out+nout,"\t");
554 if ( tag->key[0]!=' ' || tag->key[1]!=' ' )
555 nout += sprintf(out+nout,"%c%c:", tag->key[0],tag->key[1]);
556 nout += sprintf(out+nout,"%s", tag->value);
557 tags = tags->next;
558 }
559 hlines = hlines->next;
560 nout += sprintf(out+nout,"\n");
561 }
562 out[len] = 0;
563 return out;
564 }
565
566 void *sam_header_parse2(const char *headerText)
567 {
568 list_t *hlines = NULL;
569 HeaderLine *hline;
570 const char *text;
571 char *buf=NULL;
572 size_t nbuf = 0;
573 int tovalidate = 0;
574
575 if ( !headerText )
576 return 0;
577
578 text = headerText;
579 while ( (text=nextline(&buf, &nbuf, text)) )
580 {
581 hline = sam_header_line_parse(buf);
582 if ( hline && (!tovalidate || sam_header_line_validate(hline)) )
583 // With too many (~250,000) reference sequences the header parsing was too slow with list_append.
584 hlines = list_append_to_end(hlines, hline);
585 else
586 {
587 if (hline) sam_header_line_free(hline);
588 sam_header_free(hlines);
589 if ( buf ) free(buf);
590 return NULL;
591 }
592 }
593 if ( buf ) free(buf);
594
595 return hlines;
596 }
597
598 void *sam_header2tbl(const void *_dict, char type[2], char key_tag[2], char value_tag[2])
599 {
600 const HeaderDict *dict = (const HeaderDict*)_dict;
601 const list_t *l = dict;
602 khash_t(str) *tbl = kh_init(str);
603 khiter_t k;
604 int ret;
605
606 if (_dict == 0) return tbl; // return an empty (not null) hash table
607 while (l)
608 {
609 HeaderLine *hline = l->data;
610 if ( hline->type[0]!=type[0] || hline->type[1]!=type[1] )
611 {
612 l = l->next;
613 continue;
614 }
615
616 HeaderTag *key, *value;
617 key = header_line_has_tag(hline,key_tag);
618 value = header_line_has_tag(hline,value_tag);
619 if ( !key || !value )
620 {
621 l = l->next;
622 continue;
623 }
624
625 k = kh_get(str, tbl, key->value);
626 if ( k != kh_end(tbl) )
627 debug("[sam_header_lookup_table] They key %s not unique.\n", key->value);
628 k = kh_put(str, tbl, key->value, &ret);
629 kh_value(tbl, k) = value->value;
630
631 l = l->next;
632 }
633 return tbl;
634 }
635
636 char **sam_header2list(const void *_dict, char type[2], char key_tag[2], int *_n)
637 {
638 const HeaderDict *dict = (const HeaderDict*)_dict;
639 const list_t *l = dict;
640 int max, n;
641 char **ret;
642
643 ret = 0; *_n = max = n = 0;
644 while (l)
645 {
646 HeaderLine *hline = l->data;
647 if ( hline->type[0]!=type[0] || hline->type[1]!=type[1] )
648 {
649 l = l->next;
650 continue;
651 }
652
653 HeaderTag *key;
654 key = header_line_has_tag(hline,key_tag);
655 if ( !key )
656 {
657 l = l->next;
658 continue;
659 }
660
661 if (n == max) {
662 max = max? max<<1 : 4;
663 ret = realloc(ret, max * sizeof(void*));
664 }
665 ret[n++] = key->value;
666
667 l = l->next;
668 }
669 *_n = n;
670 return ret;
671 }
672
673 void *sam_header2key_val(void *iter, const char type[2], const char key_tag[2], const char value_tag[2], const char **_key, const char **_value)
674 {
675 list_t *l = iter;
676 if ( !l ) return NULL;
677
678 while (l)
679 {
680 HeaderLine *hline = l->data;
681 if ( hline->type[0]!=type[0] || hline->type[1]!=type[1] )
682 {
683 l = l->next;
684 continue;
685 }
686
687 HeaderTag *key, *value;
688 key = header_line_has_tag(hline,key_tag);
689 value = header_line_has_tag(hline,value_tag);
690 if ( !key && !value )
691 {
692 l = l->next;
693 continue;
694 }
695
696 *_key = key->value;
697 *_value = value->value;
698 return l->next;
699 }
700 return l;
701 }
702
703 const char *sam_tbl_get(void *h, const char *key)
704 {
705 khash_t(str) *tbl = (khash_t(str)*)h;
706 khint_t k;
707 k = kh_get(str, tbl, key);
708 return k == kh_end(tbl)? 0 : kh_val(tbl, k);
709 }
710
711 int sam_tbl_size(void *h)
712 {
713 khash_t(str) *tbl = (khash_t(str)*)h;
714 return h? kh_size(tbl) : 0;
715 }
716
717 void sam_tbl_destroy(void *h)
718 {
719 khash_t(str) *tbl = (khash_t(str)*)h;
720 kh_destroy(str, tbl);
721 }
722
723 void *sam_header_merge(int n, const void **_dicts)
724 {
725 const HeaderDict **dicts = (const HeaderDict**)_dicts;
726 HeaderDict *out_dict;
727 int idict, status;
728
729 if ( n<2 ) return NULL;
730
731 out_dict = sam_header_clone(dicts[0]);
732
733 for (idict=1; idict<n; idict++)
734 {
735 const list_t *tmpl_hlines = dicts[idict];
736
737 while ( tmpl_hlines )
738 {
739 list_t *out_hlines = out_dict;
740 int inserted = 0;
741 while ( out_hlines )
742 {
743 status = sam_header_compare_lines(tmpl_hlines->data, out_hlines->data);
744 if ( status==0 )
745 {
746 out_hlines = out_hlines->next;
747 continue;
748 }
749
750 if ( status==2 )
751 {
752 print_header_line(stderr,tmpl_hlines->data);
753 print_header_line(stderr,out_hlines->data);
754 debug("Conflicting lines, cannot merge the headers.\n");
755 return 0;
756 }
757 if ( status==3 )
758 sam_header_line_merge_with(out_hlines->data, tmpl_hlines->data);
759
760 inserted = 1;
761 break;
762 }
763 if ( !inserted )
764 out_dict = list_append(out_dict, sam_header_line_clone(tmpl_hlines->data));
765
766 tmpl_hlines = tmpl_hlines->next;
767 }
768 }
769
770 return out_dict;
771 }
772
773 char **sam_header2tbl_n(const void *dict, const char type[2], const char *tags[], int *n)
774 {
775 int nout = 0;
776 char **out = NULL;
777
778 *n = 0;
779 list_t *l = (list_t *)dict;
780 if ( !l ) return NULL;
781
782 int i, ntags = 0;
783 while ( tags[ntags] ) ntags++;
784
785 while (l)
786 {
787 HeaderLine *hline = l->data;
788 if ( hline->type[0]!=type[0] || hline->type[1]!=type[1] )
789 {
790 l = l->next;
791 continue;
792 }
793 out = (char**) realloc(out, sizeof(char*)*(nout+1)*ntags);
794 for (i=0; i<ntags; i++)
795 {
796 HeaderTag *key = header_line_has_tag(hline, tags[i]);
797 if ( !key )
798 {
799 out[nout*ntags+i] = NULL;
800 continue;
801 }
802 out[nout*ntags+i] = key->value;
803 }
804 nout++;
805 l = l->next;
806 }
807 *n = nout;
808 return out;
809 }
810