forked from samtools/samtools
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathADNI_interactive.c
5130 lines (4666 loc) · 146 KB
/
ADNI_interactive.c
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
/* ==============================================================================
Specific additions built on top of samtools to visualize several
aligned bam files or GTL files directly in the terminal.
by N.Guex and C.Iseli 2014-2019
Copyright (C) SIB - Swiss Institute of Bioinformatics, 2014-2019 Nicolas Guex and Christian Iseli
Copyright (C) UNIL - University of Lausanne, Switzerland 2019 Nicolas Guex and Christian Iseli
Copyright (C) EPFL - Ecole Polytechnique Fédérale de Lausanne, Switzerland 2021 Christian Iseli
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
Code: Nicolas Guex and Christian Iseli
Contacts: Nicolas.Guex@unil.ch and christian.iseli@epfl.ch
Repository: https://github.com/sib-swiss/samtools
============================================================================== */
/*
this source file contains portions of code taken from
sam_view.c -- SAM<->BAM<->CRAM conversion.
Copyright (C) 2009-2014 Genome Research Ltd.
Portions copyright (C) 2009, 2011, 2012 Broad Institute.
Author: Heng Li <lh3@sanger.ac.uk>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notices and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */
#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <unistd.h>
#include <inttypes.h>
#include "htslib/sam.h"
#include "htslib/bgzf.h"
#include <sys/time.h>
#include <termios.h>
#include <sys/ioctl.h>
#include <signal.h>
#include <dirent.h>
#include <pthread.h>
#include <ctype.h>
#include <sys/types.h>
#include <regex.h>
// --------------------------------------------------------------------------------------------------
//#define ROBIN /* specific version made for Robin Liechti to support a tool in use at the HUG */
// --------------------------------------------------------------------------------------------------
#ifdef ROBIN
#define kHalfGenomicChunk 2048 // max without changing the way I grab the genomic seq with fetch is 15000...
#define kMaxTagsXScreens 524288
#define CLEVER_STORE_INSERTIONS
static int gRobinPrintEveryNthLine = 1;
#else
#define kHalfGenomicChunk 10000 // max without changing the way I grab the genomic seq with fetch is 15000...
//define kMaxTagsXScreens 0x400000 /* guesstimate; this eats roughly 64 gigs of virtual mem (and real mem if reads are loaded) */
#define kMaxTagsXScreens 0x100000 /* guesstimate; this eats roughly 16 gigs of virtual mem (and real mem if reads are loaded) */
//define kMaxTagsXScreens 0x80000 /* guesstimate; this eats roughly 8 gigs of virtual mem (and real mem if reads are loaded) */
#endif
#define kGenomicChunk (kHalfGenomicChunk*2)
#define kMaxLineBuf 32767
#define kMaxDir 1024
#define kMaxFileName 512
#define kMaxBamName 64
#ifdef ROBIN
#define kMaxTagLength 1024
#define kMaxScreenCol 1024
#else
//define kMaxTagLength 8192
#define kMaxTagLength (2*8192 + 4096)
#define kMaxScreenCol 1024
#endif
#define kMaxTagInsertion 256
#define kMaxTagnameLength 48
#define kMaxTagOrdinalLength 12
//define kMaxVirutalScreen 24
#define kMaxVirutalScreen 9
#define kScreenPanelMargin 5
#define kColOffset 5
#define kMaxPatients 1024
#define kIsPairedEnd 0xFFFF
#define kIsBAM 0x1
#define kIsGTL 0x2
#define kIsTB 0x4
#define kIsMPEGG 0x8
#define kShowTagName 1
#define kShowQuality 2
#define kMaskLowQuality 4
#define kShowSNP 8 // FIXME - probably not so useful to turn this off ? could be always on... free the v key
#define kSplitScreen 16
#define kDisplayPatientID 32
#define kZoomActivePanel 64
#define kExplorePhenotype 128
#define kHideSameMapping 256
#define kShowTagOrdinal 512
#define kFilterAllele 1024
#define kShowCoverage 2048
#define kZoomCoverage 4096
#define kReadCoverage 8192
#define kFilterClone 16384
#define kShowSequence 32768
#define kVirtScreenMaxLines 768
// --------------------------------------------------------------------------------------------------
static unsigned int gNbVirtualScreen;
static unsigned int gMaxTags;
static int gNoCompare;
static int gNoChrInBAM;
static char gGTLgenome[kMaxFileName];
static char gGTLbindir[kMaxFileName];
static char alignerConfigFile[kMaxFileName];
static char *gShowAnnotation;
typedef struct _chr_pos_t {
unsigned int offset;
unsigned int len;
char name[32];
} chr_pos_t;
chr_pos_t chrPos[32];
unsigned int nbChrPos;
static char gFilterAlleleNT;
static unsigned int gFilterAllelePos;
static void usage(void);
static void help(void);
static void SIGQUITcatch (int sig);
//#define DEBUGOUTPUT
#ifdef DEBUGOUTPUT
static FILE *debug;
#endif
// --------------------------------------------------------------------------------------------------
typedef struct PATIENT_struct PATIENT;
struct PATIENT_struct
{
char bamfile[32];
char patient[16];
int color;
};
typedef struct TAG_struct TAG;
struct TAG_struct
{
unsigned long ordinal;
char tagname[kMaxTagnameLength];
char tagseq[kMaxTagLength];
char tagqual[kMaxTagLength];
char taginsertion[kMaxTagInsertion]; // FIXME: hack to store original tag
char taginsertionQual[kMaxTagInsertion]; // FIXME: hack to store original tag quality.
unsigned int tagpos;
int tagpair; // in case of single end, a value of 1 indicate sit maps on the reverse strand
int tagLength;
int flag;
int screenline;
};
typedef struct SNPTABLE_struct SNPTABLE;
struct SNPTABLE_struct
{
int chr;
int pos;
int bgCode;
int fgCode;
};
typedef struct _NAV_struct {
SNPTABLE *loc;
unsigned int max;
unsigned int cur;
unsigned int nb;
} NAV;
static NAV SNPpos;
static NAV recSNPpos;
static NAV geneSearchPos;
static NAV genomeSearchPos;
static NAV *curNPpos;
#define kCoverageElements 8
typedef struct BAMFILE_struct BAMFILE;
struct BAMFILE_struct
{
samFile *in;
bam1_t *b;
bam_hdr_t *header;
hts_idx_t *idx;
hts_itr_t *iter;
unsigned short coverage[kCoverageElements * (kGenomicChunk+kMaxScreenCol)];
unsigned int maxCoverage;
unsigned int medianCoverage;
unsigned int mostFrequentFragmentSize;
unsigned int startPos;
unsigned int retained;
unsigned int readTags;
int curbam;
char patientname[16];
char ADNIbamname[24];
char displayname[16];
char info[64];
char fn[kMaxFileName];
int cursnp;
int color;
int fileformat;
};
typedef struct VIRTUALSCREEN_struct VIRTUALSCREEN;
struct VIRTUALSCREEN_struct
{
char *virtualscreen;
unsigned int linelength[kVirtScreenMaxLines];
unsigned int printed;
unsigned int linecnt;
};
typedef struct EXECUTIONPLAN_struct EXECUTIONPLAN;
struct EXECUTIONPLAN_struct
{
BAMFILE *bam;
TAG *tag;
int chr;
unsigned int pos;
int rslt;
int screenpanel;
};
static int verbose = 0;
static char genome[kMaxLineBuf+1];
static char gAnnotationFwd[kMaxLineBuf+1];
static char gAnnotationRev[kMaxLineBuf+1];
static char gAnnotationGene[kMaxLineBuf+1];
static int volatile keeprunning = 1;
static int showmode = kShowSNP | kShowCoverage | kFilterClone;
static int gMaxTagNameLength = 0;
static int gScreenCnt = 1;
static int singleEnd = 0;
static char gLowQualityFilterThreshold = '#';
static char searchGenome[512];
#ifdef ROBIN
static int directDump = 200;
#else
static int directDump = 0;
#endif
// --------------------------------------------------------------------------------------------------
// code adapted from bam_read1 that can be found in ../htslib/sam.c
// warning: removed the big endian test.
//
static int bam_readADNI(BGZF *fp, bam1_t *b)
{
bam1_core_t *c = &b->core;
int32_t block_len, ret;
uint32_t x[8];
if ((ret = bgzf_read(fp, &block_len, 4)) != 4)
{
if (ret == 0)
return -1; // normal end-of-file
else
return -2; // truncated
}
if (bgzf_read(fp, x, 32) != 32)
return -3;
c->tid = x[0];
c->pos = x[1];
c->bin = x[2]>>16;
c->qual = x[2]>>8&0xff;
c->l_qname = x[2]&0xff;
c->flag = x[3]>>16;
c->n_cigar = x[3]&0xffff;
c->l_qseq = x[4];
c->mtid = x[5];
c->mpos = x[6];
c->isize = x[7];
b->l_data = block_len - 32;
if (b->l_data < 0 || c->l_qseq < 0)
return -4;
if ((char *)bam_get_aux(b) - (char *)b->data > b->l_data)
return -4;
if (b->m_data < b->l_data)
{
b->m_data = b->l_data;
kroundup32(b->m_data);
b->data = (uint8_t*)realloc(b->data, b->m_data);
if (!b->data)
return -4;
}
if (bgzf_read(fp, b->data, b->l_data) != b->l_data)
return -4;
return 4 + block_len;
} /* bam_readADNI */
// --------------------------------------------------------------------------------------------------
static void
getCoverage(int pos, BAMFILE *bam, TAG *tag, int *lastP)
{
unsigned int sp = 0;
int p = tag->tagpos - pos;
int reverse = 0;
if ((singleEnd && tag->tagpair) || (tag->flag & 0x91) == 0x91 || (tag->flag & 0x51) == 0x41)
reverse = 1;
if (*lastP != 0 && p > *lastP && !(showmode & kReadCoverage))
{
int i;
int max = p;
if (max > kGenomicChunk+kMaxScreenCol)
max = kGenomicChunk+kMaxScreenCol;
for (i = *lastP; i < max; i++)
{
if (bam->coverage[i * kCoverageElements + 6] < 0xFFFFU)
bam->coverage[i * kCoverageElements + 6] += 1;
if (reverse && bam->coverage[i * kCoverageElements + 7] < 0xFFFFU)
bam->coverage[i * kCoverageElements + 7] += 1;
}
}
while (tag->tagseq[sp] != 0)
{
if (p >= kGenomicChunk+kMaxScreenCol)
break;
if (p >= 0)
{
unsigned int idx = p * kCoverageElements;
// do not count twice when the 2 fragments overlap
if (p >= *lastP)
{
unsigned int v = 0;
switch (tag->tagseq[sp]) {
case 'A': break;
case 'a': break;
case 'C': v = 1; break;
case 'c': v = 1; break;
case 'G': v = 2; break;
case 'g': v = 2; break;
case 'T': v = 3; break;
case 't': v = 3; break;
case '_': v = 4; break;
case '*': v = 5; break;
default: v = 6;
}
if (bam->coverage[idx + v] < 0xFFFFU)
bam->coverage[idx + v] += 1;
if (reverse && bam->coverage[idx + 7] < 0xFFFFU)
bam->coverage[idx + 7] += 1;
}
}
sp += 1;
p += 1;
}
if (p > 0)
*lastP = p;
else
*lastP = 1;
}
static int compare_short(const void *a, const void *b)
{
short sa = *(short *)a;
short sb = *(short *)b;
if (sa < sb)
return -1;
if (sa > sb)
return 1;
return 0;
}
// --------------------------------------------------------------------------------------------------
// code adapted from sam_read1 that can be found in ../htslib/sam.c
//
static int sam_readADNI(BAMFILE *bam,bam1_t *b,TAG *tag, int pos, int maxpos)
{
int curChr = -1; // when negative, means error.
int r;
unsigned int retained = 0;
unsigned int readTags = 0;
int dbg = 0;
if (verbose >= 9 && dbg == 1)
fprintf(stderr,"entering sam_readADNI maxpos = %d for %s\n",maxpos,bam->fn);
if (bam->iter) // jump to first entry of requested chromosome.
{
r=sam_itr_next(bam->in, bam->iter, b);
goto process;
}
while ((r=bam_readADNI((bam->in)->fp.bgzf, b)) >= 0)
{
process:;
if (r >= 0)
{
if (b->core.tid >= (bam->header)->n_targets || b->core.tid < -1 ||
b->core.mtid >= (bam->header)->n_targets || b->core.mtid < -1)
{
curChr = -3;
goto done;
}
}
/* ------- do our processing ---------- */
const bam1_core_t *c = &b->core;
if (c->qual >= 0 && c->n_cigar && c->l_qseq) // only keep good quality with cigar info and sequence
{
int i;
if (c->tid != curChr) // chr change.
{
if (curChr != -1)
goto done;
curChr = c->tid;
}
if (verbose >= 9 && dbg == 1)
fprintf(stderr,"readTags = %d; c->pos = %zd\n",readTags, (ssize_t) (c->pos));
#ifdef DEBUGOUTPUT
fprintf(debug,"readTags = %d; c->pos = %d\n",readTags, c->pos);
#endif
if (c->pos > maxpos)
goto done;
readTags++;
uint32_t *cigar = bam_get_cigar(b);
for (i = 0; i < b->core.n_cigar; i++) // do not treat I and P for now.
{
// if (bam_cigar_opchr(cigar[i]) == 'I')
// break;
if (bam_cigar_opchr(cigar[i]) == 'P')
break;
}
if (i == b->core.n_cigar) // ok to keep.
//if ((bam_cigar_opchr(cigar[0]) == 'M') && (bam_cigar_oplen(cigar[0]) == kTagLength))
{
if (b->core.l_qname > gMaxTagNameLength) // WARN multiple threads can concurr here to alter this variable.
gMaxTagNameLength = b->core.l_qname;
strncpy(tag[retained].tagname,bam_get_qname(b),b->core.l_qname);
for (i = (b->core.l_qname-1); i< kMaxTagnameLength-1/*gMaxTagNameLength*/;i++)
tag[retained].tagname[i] = ' ';
tag[retained].tagname[kMaxTagnameLength-1] = '\0';
//tag[retained].tagname[b->core.l_qname+2] = '\0';
uint8_t *s = bam_get_seq(b);
uint8_t *q = bam_get_qual(b);
//if (s[0] == 0xff) kputc('*', str); case should never happen ?
int dstp = 0;
int srcp = 0;
int ok = 0;
tag[retained].ordinal = 0;
tag[retained].taginsertion[0] = '\0';
tag[retained].taginsertionQual[0] = '\0';
#ifdef CLEVER_STORE_INSERTIONS
int ip=0;
#endif
for (i = 0; i < c->n_cigar; ++i)
{
int k;
switch(bam_cigar_opchr(cigar[i]))
{
case 'H':
//for (k = 0; k < bam_cigar_oplen(cigar[i]); k++)
//{
// srcp++;
//}
// actually - do nothing...
break;
case 'M':
for (k = 0; k < bam_cigar_oplen(cigar[i]); k++)
{
tag[retained].tagseq[dstp] = "=ACMGRSVTWYHKDBN"[bam_seqi(s, srcp)];
tag[retained].tagqual[dstp] = (char)(q[srcp] + 33);
dstp++;
srcp++;
if (dstp == kMaxTagLength)
goto ignore;
}
break;
case 'S': // soft clipping. coordinate of match is
for (k = 0; k < bam_cigar_oplen(cigar[i]); k++)
{
srcp++;
}
break;
case 'D':
for (k = 0; k < bam_cigar_oplen(cigar[i]); k++)
{
tag[retained].tagseq[dstp] = '_';
tag[retained].tagqual[dstp] = '_';
dstp++;
if (dstp == kMaxTagLength)
{
fprintf(stderr,"Warning, tag %s ignored expanded length kMaxTagLength\n",tag[retained].tagname);
goto ignore;
}
}
break;
case 'N':
for (k = 0; k < bam_cigar_oplen(cigar[i]); k++)
{
tag[retained].tagseq[dstp] = 'i';
tag[retained].tagqual[dstp] = 'i';
dstp++;
if (dstp == kMaxTagLength)
{
fprintf(stderr,"Warning, tag %s ignored expanded length kMaxTagLength N %d\n",tag[retained].tagname, bam_cigar_oplen(cigar[i]));
goto ignore;
}
}
break;
case 'I':
//printf("Warning, tag %s has insertion\n",tag[retained].tagname);
// should find a way to store the insertion !!!
#ifdef CLEVER_STORE_INSERTIONS
// mark presence of new insertion stored after the '|' mark.
tag[retained].taginsertion[ip] = '|';
tag[retained].taginsertionQual[ip] = '|';
ip++;
#endif
for (k = 0; k < bam_cigar_oplen(cigar[i]); k++)
{
#ifdef CLEVER_STORE_INSERTIONS
tag[retained].taginsertion[ip] = "=ACMGRSVTWYHKDBN"[bam_seqi(s, srcp)];
tag[retained].taginsertionQual[ip] = (char)(q[srcp] + 33);
ip++;
#endif
srcp++;
}
#ifdef CLEVER_STORE_INSERTIONS
tag[retained].taginsertion[ip] = '\0';
tag[retained].taginsertionQual[ip] = '\0';
#else
// proposed way to store insertion, not particularly clever: save original tag.
for (k=0; k < c->l_qseq && k < (kMaxTagInsertion - 1);k++)
{
tag[retained].taginsertion[k] = "=ACMGRSVTWYHKDBN"[bam_seqi(s, k)];
tag[retained].taginsertionQual[k] = (char)(q[k] + 33);
}
tag[retained].taginsertion[k] = '\0';
tag[retained].taginsertionQual[k] = '\0';
#endif
tag[retained].tagseq[dstp-1] = '*';
tag[retained].tagqual[dstp-1] = '*';
break;
default:
goto ignore;
break;
}
}
ok = 1;
ignore:
if (ok)
{
tag[retained].tagseq[dstp] = '\0';
tag[retained].tagqual[dstp] = '\0';
tag[retained].tagpos = c-> pos;
tag[retained].tagLength = dstp; //c->l_qseq;
tag[retained].flag = c->flag;
if (!singleEnd)
{
tag[retained].tagpair = -1;
if (c->mpos <= c->pos) // worth looking for the mate...
{
if (verbose >= 9 && dbg == 1)
fprintf(stderr,"%zd <= %zd\n",(ssize_t) (c->mpos),(ssize_t) (c->pos));
i = retained-1;
while (i >= 0)
{
if (verbose >= 9 && dbg == 1)
fprintf(stderr,"'%s'\n'%s'\n\n",tag[i].tagname,tag[retained].tagname);
if (strcmp(tag[i].tagname,tag[retained].tagname) == 0)
{
tag[i].tagpair = retained;
tag[retained].tagpair = i;
break;
}
i--;
}
}
if (verbose >= 9 && dbg == 1)
fprintf(stderr,"%u\t%d\t%s\t%s\t%u\t%u\t%.20s; mpos %zd pos %zd\n",retained,tag[retained].tagpair,tag[retained].tagname,(bam->header)->target_name[c->tid],tag[retained].tagpos,c->qual,tag[retained].tagseq,(ssize_t) (c->mpos),(ssize_t) (c->pos));
}
else
{
if (b->core.flag & BAM_FREVERSE)
tag[retained].tagpair = 1;
else
tag[retained].tagpair = 0;
if (verbose >= 9 && dbg == 1)
fprintf(stderr,"%u\t%d\t%s\t%s\t%u\t%u\t%.20s; mpos %zd pos %zd\n",retained,tag[retained].tagpair,tag[retained].tagname,(bam->header)->target_name[c->tid],tag[retained].tagpos,c->qual,tag[retained].tagseq,(ssize_t) (c->mpos),(ssize_t) (c->pos));
}
retained++;
} // ok
if (retained == gMaxTags)
{
fprintf(stderr,"ERROR: reached max tags (%d) ; should realloc buffer !!!!! %d\n",retained,gMaxTags);
fflush(stdout);
exit(1);
break;
}
}
}
} // while
done:;
memset(bam->coverage,0,kCoverageElements * (kGenomicChunk+kMaxScreenCol) * sizeof(short));
for (r = 0; r < retained; r++)
{
int lastP = 0;
if (!singleEnd)
{
if (tag[r].tagpair == -1)
{
getCoverage(pos, bam, tag + r, &lastP);
}
else if (tag[r].tagpair > r)
{
getCoverage(pos, bam, tag + r, &lastP);
getCoverage(pos, bam, tag + tag[r].tagpair, &lastP);
}
}
else
{
getCoverage(pos, bam, tag + r, &lastP);
}
}
bam->startPos = pos;
bam->maxCoverage = 0;
unsigned short tem[kGenomicChunk+kMaxScreenCol];
unsigned int tc = 0;
for (r = 0; r < kCoverageElements * (kGenomicChunk+kMaxScreenCol); r += kCoverageElements)
{
unsigned int cov = bam->coverage[r] + bam->coverage[r+1] + bam->coverage[r+2] + bam->coverage[r+3] + bam->coverage[r+4] + bam->coverage[r+5] + bam->coverage[r+6];
// put some figure.. enough to get out of noise in exome, but not too much...
if (cov > 7)
tem[tc++] = cov;
if (cov > bam->maxCoverage)
bam->maxCoverage = cov;
}
qsort(tem,tc,2,compare_short);
bam->medianCoverage = 1;
if (tc > 0)
bam->medianCoverage = tem[tc/2];
bam->retained = retained;
bam->readTags = readTags;
return (curChr);
} /* sam_readADNI */
// --------------------------------------------------------------------------------------------------
static char *bf;
static int compareFilenames(const void *a, const void *b)
{
return strcmp(&bf[(*(int*)a) *kMaxBamName], &bf[(*(int*)b) *kMaxBamName]);
}
// --------------------------------------------------------------------------------------------------
static void sortbamNames(char *bamfiles,int bamcnt)
{
int idx[kMaxDir];
int i;
char *tmp = NULL;
int err;
err = posix_memalign((void **)&tmp, 64, bamcnt*kMaxBamName*sizeof(char));
if (err == 0)
{
for (i = 0; i< bamcnt; i++)
{
idx[i] = i;
memcpy(&tmp[i*kMaxBamName],&bamfiles[i*kMaxBamName],kMaxBamName);
}
bf = &bamfiles[0];
qsort(idx, bamcnt, sizeof(int), compareFilenames);
for (i = 0; i< bamcnt; i++)
{
memcpy(&bamfiles[i*kMaxBamName],&tmp[idx[i]*kMaxBamName],kMaxBamName);
}
free(tmp);
}
} /* sortbamNames */
// --------------------------------------------------------------------------------------------------
#define kCompStringLen (kMaxTagnameLength+16) /* note add 16 to hold chr mapping position */
static char *tn;
static int compareTagnames(const void *a, const void *b)
{
return strcmp(&tn[(*(int*)a) *kCompStringLen], &tn[(*(int*)b) *kCompStringLen]);
}
// --------------------------------------------------------------------------------------------------
// FIXME! not crash free. no testing for stringlength etc...
static void compareAlignments(TAG *reftag, TAG *tag,int reftagcnt,int tagcnt)
{
char *tmp = NULL;
int refidx[reftagcnt];
int idx[tagcnt];
int tagidx;
int err;
#ifdef DEBUGOUTPUT
FILE *LOG = NULL;
#endif
if (gNoCompare || !(showmode & kSplitScreen))
return;
if (gScreenCnt != 2)
return;
#ifdef DEBUGOUTPUT
LOG = fopen("/tmp/ADVIEWlog.txt","w");
#endif
//----------- sort ref tags
err = posix_memalign((void **)&tmp, 64, reftagcnt*kCompStringLen*sizeof(char));
if (err != 0)
return;
for (tagidx = 0; tagidx < reftagcnt; tagidx++)
{
refidx[tagidx] = tagidx;
//memcpy(&tmp[tagidx*kCompStringLen],&reftag[tagidx].tagname[0],kCompStringLen);
sprintf(&tmp[tagidx*kCompStringLen],"%s%u",&reftag[tagidx].tagname[0],reftag[tagidx].tagpos); // FIXME! potential crash possible ?
}
tn = &tmp[0];
qsort(refidx, reftagcnt, sizeof(int), compareTagnames);
free(tmp);
// --------- sort tags
err = posix_memalign((void **)&tmp, 64, tagcnt*kCompStringLen*sizeof(char));
if (err != 0)
return;
for (tagidx = 0; tagidx < tagcnt; tagidx++)
{
idx[tagidx] = tagidx;
//memcpy(&tmp[tagidx*kCompStringLen],&tag[tagidx].tagname[0],kCompStringLen);
sprintf(&tmp[tagidx*kCompStringLen],"%s%u",&tag[tagidx].tagname[0],tag[tagidx].tagpos); // FIXME! potential crash possible ?
}
tn = &tmp[0];
qsort(idx, tagcnt, sizeof(int), compareTagnames);
free(tmp);
// ---------- print.
int i = 0;
tagidx = 0;
#ifdef DEBUGOUTPUT
fprintf(LOG,"COMPARING TAGNAMES\n'%s'\n'%s'\n\n",&reftag[refidx[tagidx]].tagname[0],&tag[idx[i] ].tagname[0]);
#endif
while(1)
{
char *spr1 = strchr(&reftag[refidx[tagidx ]].tagname[0], ' ');
char *spr2 = strchr(&reftag[refidx[tagidx+1]].tagname[0], ' ');
char *spt1 = strchr( &tag[idx[i] ].tagname[0], ' ');
char *spt2 = strchr( &tag[idx[i+1] ].tagname[0], ' ');
int lr1 = (spr1 != NULL) ? spr1 - reftag[refidx[tagidx]].tagname : kMaxTagnameLength;
int lr2 = (spr2 != NULL) ? spr2 - reftag[refidx[tagidx+1]].tagname : kMaxTagnameLength;
int lt1 = (spt1 != NULL) ? spt1 - tag[idx[i]].tagname : kMaxTagnameLength;
int lt2 = (spt2 != NULL) ? spt2 - tag[idx[i+1]].tagname : kMaxTagnameLength;
int lc = (lr1 >= lt1) ? lr1 : lt1;
int lc1 = (lr1 >= lr2) ? lr1 : lr2;
int lc2 = (lt1 >= lt2) ? lt1 : lt2;
int cmp = strncmp(&reftag[refidx[tagidx]].tagname[0], &tag[idx[i] ].tagname[0],lc);
int cmp1 = strncmp(&reftag[refidx[tagidx]].tagname[0],&reftag[refidx[tagidx+1]].tagname[0],lc1);
int cmp2 = strncmp(&tag[idx[i] ].tagname[0], &tag[idx[i+1] ].tagname[0],lc2);
// same tag, pair found in ref and in query.
if (cmp == 0 && cmp1 == 0 && cmp2 == 0)
{
#ifdef DEBUGOUTPUT
fprintf(LOG,"%5d / %5d) %5d %s pos=%u = (%d) %s pos=%u\n",tagidx,reftagcnt,refidx[tagidx],&reftag[refidx[tagidx]].tagname[0],reftag[refidx[tagidx]].tagpos,i,&tag[idx[i]].tagname[0],tag[idx[i]].tagpos);
fprintf(LOG,"%5d / %5d) %5d %s pos=%u = (%d) %s pos=%u\n\n",tagidx,reftagcnt,refidx[tagidx],&reftag[refidx[tagidx+1]].tagname[0],reftag[refidx[tagidx+1]].tagpos,i,&tag[idx[i+1]].tagname[0],tag[idx[i+1]].tagpos);
#endif
if (reftag[refidx[tagidx]].tagpos == tag[idx[i]].tagpos)
{
memcpy(&reftag[refidx[tagidx]].tagname[0]," ok ",6);
memcpy(&tag[idx[i]].tagname[0] ," ok ",6);
}
else
{
memcpy(&reftag[refidx[tagidx]].tagname[0]," ~ok~ ",6);
memcpy(&tag[idx[i]].tagname[0] ," ~ok~ ",6);
}
if (reftag[refidx[tagidx+1]].tagpos == tag[idx[i+1]].tagpos)
{
memcpy(&reftag[refidx[tagidx]].tagname[6]," ok ",6);
memcpy(&tag[idx[i]].tagname[6] ," ok ",6);
}
else
{
memcpy(&reftag[refidx[tagidx]].tagname[6]," ~ok~ ",6);
memcpy(&tag[idx[i]].tagname[6] ," ~ok~ ",6);
}
#ifdef DEBUGOUTPUT
fprintf(LOG,"%5d / %5d) %5d %s pos=%u = (%d) %s pos=%u\n",tagidx,reftagcnt,refidx[tagidx],&reftag[refidx[tagidx]].tagname[0],reftag[refidx[tagidx]].tagpos,i,&tag[idx[i]].tagname[0],tag[idx[i]].tagpos);
fprintf(LOG,"%5d / %5d) %5d %s pos=%u = (%d) %s pos=%u\n\n",tagidx,reftagcnt,refidx[tagidx],&reftag[refidx[tagidx+1]].tagname[0],reftag[refidx[tagidx+1]].tagpos,i,&tag[idx[i+1]].tagname[0],tag[idx[i+1]].tagpos);
#endif
tagidx +=2;
i +=2;
}
// same tag, pair found only in ref.
else if (cmp == 0 && cmp1 == 0 && cmp2 != 0)
{
#ifdef DEBUGOUTPUT
fprintf(LOG,"%5d / %5d) %5d %s pos=%u = (%d) %s pos=%u\n",tagidx,reftagcnt,refidx[tagidx],&reftag[refidx[tagidx]].tagname[0],reftag[refidx[tagidx]].tagpos,i,&tag[idx[i]].tagname[0],tag[idx[i]].tagpos);
fprintf(LOG,"%5d / %5d) %5d %s pos=%u 1 (%d) %s pos=%u\n\n",tagidx,reftagcnt,refidx[tagidx],&reftag[refidx[tagidx+1]].tagname[0],reftag[refidx[tagidx+1]].tagpos,i,&tag[idx[i+1]].tagname[0],tag[idx[i+1]].tagpos);
#endif
if (reftag[refidx[tagidx]].tagpos == tag[idx[i]].tagpos)
{
memcpy(&reftag[refidx[tagidx]].tagname[0]," ok ",6);
memcpy(&tag[idx[i]].tagname[0] ," ok ",6);
}
else if (reftag[refidx[tagidx+1]].tagpos == tag[idx[i]].tagpos)
{
memcpy(&reftag[refidx[tagidx]].tagname[6]," ok ",6);
memcpy(&tag[idx[i]].tagname[6] ," ok ",6);
}
else
{
memcpy(&reftag[refidx[tagidx]].tagname[0]," ~ok~ ",6);
memcpy(&tag[idx[i]].tagname[0] ," ~ok~ ",6);
}
#ifdef DEBUGOUTPUT
fprintf(LOG,"%5d / %5d) %5d %s pos=%u = (%d) %s pos=%u\n",tagidx,reftagcnt,refidx[tagidx],&reftag[refidx[tagidx]].tagname[0],reftag[refidx[tagidx]].tagpos,i,&tag[idx[i]].tagname[0],tag[idx[i]].tagpos);
fprintf(LOG,"%5d / %5d) %5d %s pos=%u 1 (%d) %s pos=%u\n\n",tagidx,reftagcnt,refidx[tagidx],&reftag[refidx[tagidx+1]].tagname[0],reftag[refidx[tagidx+1]].tagpos,i,&tag[idx[i+1]].tagname[0],tag[idx[i+1]].tagpos);
#endif
tagidx +=2;
i++;
}
// same tag, pair found only in query
else if (cmp == 0 && cmp1 != 0 && cmp2 == 0)
{
#ifdef DEBUGOUTPUT
fprintf(LOG,"%5d / %5d) %5d %s pos=%u = (%d) %s pos=%u\n",tagidx,reftagcnt,refidx[tagidx],&reftag[refidx[tagidx]].tagname[0],reftag[refidx[tagidx]].tagpos,i,&tag[idx[i]].tagname[0],tag[idx[i]].tagpos);
fprintf(LOG,"%5d / %5d) %5d %s pos=%u 2 (%d) %s pos=%u\n\n",tagidx,reftagcnt,refidx[tagidx],&reftag[refidx[tagidx+1]].tagname[0],reftag[refidx[tagidx+1]].tagpos,i,&tag[idx[i+1]].tagname[0],tag[idx[i+1]].tagpos);
#endif
if (reftag[refidx[tagidx]].tagpos == tag[idx[i]].tagpos)
{
memcpy(&reftag[refidx[tagidx]].tagname[0]," ok ",6);
memcpy(&tag[idx[i]].tagname[0] ," ok ",6);
}
else if (reftag[refidx[tagidx]].tagpos == tag[idx[i+1]].tagpos)
{
memcpy(&reftag[refidx[tagidx]].tagname[6]," ok ",6);
memcpy(&tag[idx[i]].tagname[6] ," ok ",6);
}
else
{
memcpy(&reftag[refidx[tagidx]].tagname[0]," ~ok~ ",6);
memcpy(&tag[idx[i]].tagname[0] ," ~ok~ ",6);
}
#ifdef DEBUGOUTPUT
fprintf(LOG,"%5d / %5d) %5d %s pos=%u = (%d) %s pos=%u\n",tagidx,reftagcnt,refidx[tagidx],&reftag[refidx[tagidx]].tagname[0],reftag[refidx[tagidx]].tagpos,i,&tag[idx[i]].tagname[0],tag[idx[i]].tagpos);
fprintf(LOG,"%5d / %5d) %5d %s pos=%u 2 (%d) %s pos=%u\n\n",tagidx,reftagcnt,refidx[tagidx],&reftag[refidx[tagidx+1]].tagname[0],reftag[refidx[tagidx+1]].tagpos,i,&tag[idx[i+1]].tagname[0],tag[idx[i+1]].tagpos);
#endif
tagidx++;
i += 2;
}
else
{
if (cmp < 0)
tagidx++;
else
i++;
}
/*
// same tag ?
if (cmp == 0)
{
// same tag, same pos
if (reftag[refidx[tagidx]].tagpos == tag[idx[i]].tagpos)
{
// check if 2nd tag present
int cmp2 = strcmp(&reftag[refidx[tagidx+1]].tagname[0],&tag[idx[i+1]].tagname[0]);
if (cmp2 == 0)
{
if ((reftag[refidx[tagidx]].tagpos == tag[idx[i]].tagpos) && (reftag[refidx[tagidx+1]].tagpos == tag[idx[i+1]].tagpos))
{
memcpy(&reftag[refidx[tagidx]].tagname[0]," ok ok ",6);
memcpy(&tag[idx[i]].tagname[0] ," ok ok ",6);
}
else if ((reftag[refidx[tagidx]].tagpos == tag[idx[i]].tagpos) && (reftag[refidx[tagidx+1]].tagpos != tag[idx[i+1]].tagpos))
{
memcpy(&reftag[refidx[tagidx]].tagname[0]," ok ~ok~ ",6);
memcpy(&tag[idx[i]].tagname[0] ," ok ~ok~ ",6);
}
else if ((reftag[refidx[tagidx]].tagpos != tag[idx[i]].tagpos) && (reftag[refidx[tagidx+1]].tagpos == tag[idx[i+1]].tagpos))
{
memcpy(&reftag[refidx[tagidx]].tagname[0]," ~ok~ ok ",6);
memcpy(&tag[idx[i]].tagname[0] ," ~ok~ ok ",6);
}
else
{
memcpy(&reftag[refidx[tagidx]].tagname[0]," ~ok~ ~ok~ ",6);
memcpy(&tag[idx[i]].tagname[0] ," ~ok~ ~ok~ ",6);
}
i+=2;
tagidx+=2;
}
else if (cmp2 > 0)
{
}
else
{
}
}
// same tag != pos
else
{
strcmp(&reftag[refidx[tagidx]].tagname[0],&tag[idx[i+1]].tagname[0]);
}
int overwritepos; // decide where to write the ok (left or right tag)
int refoverwritepos; // decide where to write the ok (left or right tag)
int overwriteidx;
int refoverwriteidx;
int tp = reftag[refidx[tagidx]].tagpair;
refoverwriteidx = refidx[tagidx];
overwriteidx = idx[i];
if (reftag[refidx[tagidx]].tagpos < reftag[tp].tagpos)
refoverwritepos = 0;
else if (reftag[refidx[tagidx]].tagpos > reftag[tp].tagpos)
{
refoverwritepos = 6;
refoverwriteidx = tp;
}
else
refoverwritepos = 3;
tp = tag[idx[i]].tagpair;
if (tag[idx[i]].tagpos < tag[tp].tagpos)
{
overwritepos = 0;
}