gclib/gclib/GBam.cpp

#include "GBam.h"
#include <ctype.h>
#include "kstring.h"

//auxiliary functions for low level BAM record creation
uint8_t* realloc_bdata(bam1_t *b, int size) {
  if (b->m_data < size) {
        b->m_data = size;
        kroundup32(b->m_data);
        b->data = (uint8_t*)realloc(b->data, b->m_data);
        }
  if (b->data_len<size) b->data_len=size;
  return b->data;
}

uint8_t* dupalloc_bdata(bam1_t *b, int size) {
  //same as realloc_bdata, but does not free previous data
  //but returns it instead
  //it ALWAYS duplicates data
  b->m_data = size;
  kroundup32(b->m_data);
  uint8_t* odata=b->data;
  b->data = (uint8_t*)malloc(b->m_data);
  memcpy((void*)b->data, (void*)odata, b->data_len);
  b->data_len=size;
  return odata; //user must FREE this after
}

//from bam_import.c
extern unsigned short bam_char2flag_table[];

GBamRecord::GBamRecord(const char* qname, int32_t gseq_tid,
                 int pos, bool reverse, const char* qseq,
                 const char* cigar, const char* quals):exons(1) {
   //novel=true;
   bam_header=NULL;
   b=bam_init1();
   b->core.tid=gseq_tid;
   if (pos<=0) {
               b->core.pos=-1; //unmapped
               //if (gseq_tid<0)
               b->core.flag |= BAM_FUNMAP;
               }
          else b->core.pos=pos-1; //BAM is 0-based
   b->core.qual=255;
   int l_qseq=strlen(qseq);
   //this may not be accurate, setting CIGAR is the correct way
   //b->core.bin = bam_reg2bin(b->core.pos, b->core.pos+l_qseq-1);
   b->core.l_qname=strlen(qname)+1; //includes the \0 at the end
   memcpy(realloc_bdata(b, b->core.l_qname), qname, b->core.l_qname);
   set_cigar(cigar); //this will also set core.bin
   add_sequence(qseq, l_qseq);
   add_quals(quals); //quals must be given as Phred33
   if (reverse) { b->core.flag |= BAM_FREVERSE ; }
   }

GBamRecord::GBamRecord(const char* qname, int32_t flags, int32_t g_tid,
             int pos, int map_qual, const char* cigar, int32_t mg_tid, int mate_pos,
             int insert_size, const char* qseq, const char* quals,
             GVec<char*>* aux_strings):exons(1)  {
  //novel=true;
  bam_header=NULL;
  b=bam_init1();
  b->core.tid=g_tid;
  b->core.pos = (pos<=0) ? -1 : pos-1; //BAM is 0-based
  b->core.qual=map_qual;
  int l_qseq=strlen(qseq);
  b->core.l_qname=strlen(qname)+1; //includes the \0 at the end
  memcpy(realloc_bdata(b, b->core.l_qname), qname, b->core.l_qname);
  set_cigar(cigar); //this will also set core.bin
  add_sequence(qseq, l_qseq);
  add_quals(quals); //quals must be given as Phred33
  set_flags(flags);
  set_mdata(mg_tid, (int32_t)(mate_pos-1), (int32_t)insert_size);
  if (aux_strings!=NULL) {
    for (int i=0;i<aux_strings->Count();i++) {
       add_aux(aux_strings->Get(i));
       }
    }
}

 void GBamRecord::set_cigar(const char* cigar) {
   //requires b->core.pos and b->core.flag to have been set properly PRIOR to this call
   int doff=b->core.l_qname;
   uint8_t* after_cigar=NULL;
   int after_cigar_len=0;
   uint8_t* prev_bdata=NULL;
   if (b->data_len>doff) {
      //cigar string already allocated, replace it
      int d=b->core.l_qname + b->core.n_cigar * 4;//offset of after-cigar data
      after_cigar=b->data+d;
      after_cigar_len=b->data_len-d;
      }
   const char *s;
   char *t;
   int i, op;
   long x;
   b->core.n_cigar = 0;
   if (cigar != NULL && strcmp(cigar, "*") != 0) {
        for (s = cigar; *s; ++s) {
            if (isalpha(*s)) b->core.n_cigar++;
            else if (!isdigit(*s)) {
                 GError("Error: invalid CIGAR character (%s)\n",cigar);
                 }
            }
        if (after_cigar_len>0) { //replace/insert into existing full data
             prev_bdata=dupalloc_bdata(b, doff + b->core.n_cigar * 4 + after_cigar_len);
             memcpy((void*)(b->data+doff+b->core.n_cigar*4),(void*)after_cigar, after_cigar_len);
             free(prev_bdata);
             }
           else {
             realloc_bdata(b, doff + b->core.n_cigar * 4);
             }
        for (i = 0, s = cigar; i != b->core.n_cigar; ++i) {
            x = strtol(s, &t, 10);
            op = toupper(*t);
            if (op == 'M' || op == '=' || op == 'X') op = BAM_CMATCH;
            else if (op == 'I') op = BAM_CINS;
            else if (op == 'D') op = BAM_CDEL;
            else if (op == 'N') op = BAM_CREF_SKIP;
            else if (op == 'S') op = BAM_CSOFT_CLIP;
            else if (op == 'H') op = BAM_CHARD_CLIP;
            else if (op == 'P') op = BAM_CPAD;
            else GError("Error: invalid CIGAR operation (%s)\n",cigar);
            s = t + 1;
            bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT | op;
        }
        if (*s) GError("Error: unmatched CIGAR operation (%s)\n",cigar);
        b->core.bin = bam_reg2bin(b->core.pos, bam_calend(&b->core, bam1_cigar(b)));
    } else {//no CIGAR string given
        if (!(b->core.flag&BAM_FUNMAP)) {
            GMessage("Warning: mapped sequence without CIGAR (%s)\n", (char*)b->data);
            b->core.flag |= BAM_FUNMAP;
        }
        b->core.bin = bam_reg2bin(b->core.pos, b->core.pos + 1);
    }
   setupCoordinates();
   } //set_cigar()

 void GBamRecord::add_sequence(const char* qseq, int slen) {
   //must be called AFTER set_cigar (cannot replace existing sequence for now)
   if (qseq==NULL) return; //should we ever care about this?
   if (slen<0) slen=strlen(qseq);
   int doff = b->core.l_qname + b->core.n_cigar * 4;
   if (strcmp(qseq, "*")!=0) {
       b->core.l_qseq=slen;
       if (b->core.n_cigar && b->core.l_qseq != (int32_t)bam_cigar2qlen(&b->core, bam1_cigar(b)))
           GError("Error: CIGAR and sequence length are inconsistent!(%s)\n",
                  qseq);
       uint8_t* p = (uint8_t*)realloc_bdata(b, doff + (b->core.l_qseq+1)/2 + b->core.l_qseq) + doff;
       //also allocated quals memory
       memset(p, 0, (b->core.l_qseq+1)/2);
       for (int i = 0; i < b->core.l_qseq; ++i)
           p[i/2] |= bam_nt16_table[(int)qseq[i]] << 4*(1-i%2);
       } else b->core.l_qseq = 0;
   }

 void GBamRecord::add_quals(const char* quals) {
   //requires core.l_qseq already set
   //and must be called AFTER add_sequence(), which also allocates the memory for quals
   uint8_t* p = b->data+(b->core.l_qname + b->core.n_cigar * 4 + (b->core.l_qseq+1)/2);
   if (quals==NULL || strcmp(quals, "*") == 0) {
      for (int i=0;i < b->core.l_qseq; i++) p[i] = 0xff;
      return;
      }
   for (int i=0;i < b->core.l_qseq; i++) p[i] = quals[i]-33;
   }

 void GBamRecord::add_aux(const char* str) {
     //requires: being called AFTER add_quals()
     static char tag[2];
     static uint8_t abuf[512];
     //requires: being called AFTER add_quals()
     int strl=strlen(str);
     //int doff = b->core.l_qname + b->core.n_cigar*4 + (b->core.l_qseq+1)/2 + b->core.l_qseq + b->l_aux;
     //int doff0=doff;
     if (strl < 6 || str[2] != ':' || str[4] != ':')
         parse_error("missing colon in auxiliary data");
     tag[0] = str[0]; tag[1] = str[1];
     uint8_t atype = str[3];
     uint8_t* adata=abuf;
     int alen=0;
     if (atype == 'A' || atype == 'a' || atype == 'c' || atype == 'C') { // c and C for backward compatibility
         atype='A';
         alen=1;
         adata=(uint8_t*)&str[5];
         }
      else if (atype == 'I' || atype == 'i') {
         long long x=(long long)atoll(str + 5);
         if (x < 0) {
             if (x >= -127) {
                 atype='c';
                 abuf[0] =  (int8_t)x;
                 alen=1;
                 }
             else if (x >= -32767) {
                 atype = 's';
                 *(int16_t*)abuf = (int16_t)x;
                 alen=2;
                 }
             else {
                 atype='i';
                 *(int32_t*)abuf = (int32_t)x;
                 alen=4;
                 if (x < -2147483648ll)
                     GMessage("Parse warning: integer %lld is out of range.", x);
                 }
             } else { //x >=0
             if (x <= 255) {
                 atype = 'C';
                 abuf[0] = (uint8_t)x;
                 alen=1;
                 }
             else if (x <= 65535) {
                 atype='S';
                 *(uint16_t*)abuf = (uint16_t)x;
                 alen=2;
                 }
             else {
                 atype='I';
                 *(uint32_t*)abuf = (uint32_t)x;
                 alen=4;
                 if (x > 4294967295ll)
                     GMessage("Parse warning: integer %lld is out of range.", x);
                 }
             }
         } //integer type
         else if (atype == 'f') {
             *(float*)abuf = (float)atof(str + 5);
             alen = sizeof(float);
             }
         else if (atype == 'd') { //?
             *(float*)abuf = (float)atof(str + 9);
             alen=8;
             }
         else if (atype == 'Z' || atype == 'H') {
             if (atype == 'H') { // check whether the hex string is valid
                 if ((strl - 5) % 2 == 1) parse_error("length of the hex string not even");
                 for (int i = 0; i < strl - 5; ++i) {
                     int c = toupper(str[5 + i]);
                     if (!((c >= '0' && c <= '9') || (c >= 'A' && c <= 'F')))
                         parse_error("invalid hex character");
                     }
                 }
             memcpy(abuf, str + 5, strl - 5);
             abuf[strl-5] = 0;
             alen=strl-4;
             } else parse_error("unrecognized aux type");
  this->add_aux(tag, atype, alen, adata);
  }//add_aux()


 void GBamRecord::setupCoordinates() {
   uint32_t *cigar = bam1_cigar(b);
   const bam1_core_t *c = &b->core;
   if (c->flag & BAM_FUNMAP) return; /* skip unmapped reads */
   int l=0;
   start=c->pos+1;
   int exstart=c->pos;
   for (int i = 0; i < c->n_cigar; ++i) {
        int op = cigar[i]&0xf;
        if (op == BAM_CMATCH || op==BAM_CEQUAL ||
            op == BAM_CDIFF || op == BAM_CDEL) {
               l += cigar[i]>>4;
               }
           else if (op == BAM_CREF_SKIP) { //N
               //intron starts
               //exon ends here
               GSeg exon(exstart+1,c->pos+l);
               exons.Add(exon);
               l += cigar[i]>>4;
               exstart=c->pos+l;
               }
        }
   GSeg exon(exstart+1,c->pos+l);
   exons.Add(exon);
   end=c->pos+l;
 }

 int GBamRecord::find_tag(const char tag[2], uint8_t* & s, char& tag_type) {
   //position s at the beginning of tag "data" (after the type char)
   //returns the length of tag data, and tag type in tag_type
   s=bam1_aux(b);
   while (s < b->data + b->data_len) {
     char key[2];
     key[0] = (char)s[0]; key[1] = (char)s[1];
     s += 2; tag_type = (char)*s; ++s;
     int inc=0;
     int m_inc=0;       //for 'B' case
     uint8_t sub_type=0; // --,,--
     switch (tag_type) {
       case 'A':
       case 'C':
       case 'c':
         inc=1;
         break;
       case 'S':
       case 's':
         inc=2;
         break;
       case 'I':
       case 'i':
       case 'f':
         inc=4;
         break;
       case 'd':
         inc=8;
         break;
       case 'B':
           sub_type = *(s+1);
           int32_t n;
           memcpy(&n, s+1, 4);
           inc += 5;
           //kputc(type, &str); kputc(':', &str); kputc(sub_type, &str);
           m_inc=0;
           if (sub_type == 'c' || sub_type == 'C')
                        { m_inc=1; }
           else if (sub_type == 's' || sub_type == 'S')
                         { m_inc = 2; }
           else if ('i' == sub_type || 'I' == sub_type || 'f' == sub_type)
                         { m_inc = 4; }
           if (m_inc==0) GError("Error: invalid 'B' array subtype (%c)!\n",sub_type);
           inc += m_inc*n;
           break;
       case 'H':
       case 'Z':
         while (*(s+inc)) ++inc;
         break;
       } //switch (tag_type)
     if (tag[0]==key[0] && tag[1]==key[1])
        return inc;
     s+=inc;
     }//while aux data
   return 0;
   }

 char GBamRecord::tag_char(const char tag[2]) { //retrieve tag data as single char
   uint8_t *s;
   char tag_type=0;
   int vlen=find_tag(tag, s, tag_type);
   if (vlen==0) return 0;
   //if (vlen>1) GWarning("Warning: tag %c%c value has length %d, but char was expected.\n",
   //        tag[0],tag[1],vlen);
   return (char)s[0];
  }

 int GBamRecord::tag_int(const char tag[2]) { //get the numeric value of tag
   uint8_t *s;
   char tag_type=0;
   int vlen=find_tag(tag, s, tag_type);
   if (vlen==0) return 0;
   if (vlen==1) return (int)(*(int8_t*)s);
    else if (vlen==2) return (int)(*(int16_t*)s);
     else if (vlen==4) return (int)(*(int32_t*)s);
     else GMessage("Warning: tag %c%c value has length %d, but int type was expected.\n",
           tag[0],tag[1], vlen);
   return 0;
   }

 char* GBamRecord::tag_str(const char tag[2]) { //return string value for a tag
   uint8_t *s;
   char tag_type=0;
   int vlen=find_tag(tag, s, tag_type);
   if (vlen==0) return NULL; //not found
   //if (vlen>1) GWarning("Warning: tag %c%c value has length %d, but char was expected.\n",
   //        tag[0],tag[1],vlen);
   return (char *)s;
   }

 char GBamRecord::spliceStrand() { // '+', '-' from the XS tag, or 0 if no XS tag
   uint8_t *s;
   char tag_type=0;
   int vlen=find_tag("XS", s, tag_type);
   if (vlen==0) return '.';
   return (char)s[0];
   }

 char* GBamRecord::sequence() { //user must free this after use
   char *s = (char*)bam1_seq(b);
   char* qseq=NULL;
   GMALLOC(qseq, (b->core.l_qseq+1));
   int i;
   for (i=0;i<(b->core.l_qseq);i++) {
     int8_t v = bam1_seqi(s,i);
     qseq[i] = bam_nt16_rev_table[v];
     }
   qseq[i] = 0;
   return qseq;
   }

 char* GBamRecord::qualities() {//user must free this after use
   char *qual  = (char*)bam1_qual(b);
   char* qv=NULL;
   GMALLOC(qv, (b->core.l_qseq+1) );
   int i;
   for(i=0;i<(b->core.l_qseq);i++) {
     qv[i]=qual[i]+33;
     }
   qv[i]=0;
   return qv;
   }

 char* GBamRecord::cigar() { //returns text version of the CIGAR string; must be freed by user
   kstring_t str;
   str.l = str.m = 0; str.s = 0;
   if (b->core.n_cigar == 0) kputc('*', &str);
    else {
      for (int i = 0; i < b->core.n_cigar; ++i) {
         kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
         kputc("MIDNSHP=X"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
         }
      }
   return str.s;
   }
Revision:	133
Committed:	Fri Dec 9 15:59:14 2011 UTC (12 years, 10 months ago) by gpertea
File size:	14340 byte(s)
Log Message:	TODO: detect sam/bam input for samopen
Line	File contents
1	#include "GBam.h"
2	#include <ctype.h>
3	#include "kstring.h"
4
5	//auxiliary functions for low level BAM record creation
6	uint8_t* realloc_bdata(bam1_t *b, int size) {
7	if (b->m_data < size) {
8	b->m_data = size;
9	kroundup32(b->m_data);
10	b->data = (uint8_t*)realloc(b->data, b->m_data);
11	}
12	if (b->data_len<size) b->data_len=size;
13	return b->data;
14	}
15
16	uint8_t* dupalloc_bdata(bam1_t *b, int size) {
17	//same as realloc_bdata, but does not free previous data
18	//but returns it instead
19	//it ALWAYS duplicates data
20	b->m_data = size;
21	kroundup32(b->m_data);
22	uint8_t* odata=b->data;
23	b->data = (uint8_t*)malloc(b->m_data);
24	memcpy((void)b->data, (void)odata, b->data_len);
25	b->data_len=size;
26	return odata; //user must FREE this after
27	}
28
29	//from bam_import.c
30	extern unsigned short bam_char2flag_table[];
31
32	GBamRecord::GBamRecord(const char* qname, int32_t gseq_tid,
33	int pos, bool reverse, const char* qseq,
34	const char* cigar, const char* quals):exons(1) {
35	//novel=true;
36	bam_header=NULL;
37	b=bam_init1();
38	b->core.tid=gseq_tid;
39	if (pos<=0) {
40	b->core.pos=-1; //unmapped
41	//if (gseq_tid<0)
42	b->core.flag \|= BAM_FUNMAP;
43	}
44	else b->core.pos=pos-1; //BAM is 0-based
45	b->core.qual=255;
46	int l_qseq=strlen(qseq);
47	//this may not be accurate, setting CIGAR is the correct way
48	//b->core.bin = bam_reg2bin(b->core.pos, b->core.pos+l_qseq-1);
49	b->core.l_qname=strlen(qname)+1; //includes the \0 at the end
50	memcpy(realloc_bdata(b, b->core.l_qname), qname, b->core.l_qname);
51	set_cigar(cigar); //this will also set core.bin
52	add_sequence(qseq, l_qseq);
53	add_quals(quals); //quals must be given as Phred33
54	if (reverse) { b->core.flag \|= BAM_FREVERSE ; }
55	}
56
57	GBamRecord::GBamRecord(const char* qname, int32_t flags, int32_t g_tid,
58	int pos, int map_qual, const char* cigar, int32_t mg_tid, int mate_pos,
59	int insert_size, const char* qseq, const char* quals,
60	GVec<char> aux_strings):exons(1) {
61	//novel=true;
62	bam_header=NULL;
63	b=bam_init1();
64	b->core.tid=g_tid;
65	b->core.pos = (pos<=0) ? -1 : pos-1; //BAM is 0-based
66	b->core.qual=map_qual;
67	int l_qseq=strlen(qseq);
68	b->core.l_qname=strlen(qname)+1; //includes the \0 at the end
69	memcpy(realloc_bdata(b, b->core.l_qname), qname, b->core.l_qname);
70	set_cigar(cigar); //this will also set core.bin
71	add_sequence(qseq, l_qseq);
72	add_quals(quals); //quals must be given as Phred33
73	set_flags(flags);
74	set_mdata(mg_tid, (int32_t)(mate_pos-1), (int32_t)insert_size);
75	if (aux_strings!=NULL) {
76	for (int i=0;i<aux_strings->Count();i++) {
77	add_aux(aux_strings->Get(i));
78	}
79	}
80	}
81
82	void GBamRecord::set_cigar(const char* cigar) {
83	//requires b->core.pos and b->core.flag to have been set properly PRIOR to this call
84	int doff=b->core.l_qname;
85	uint8_t* after_cigar=NULL;
86	int after_cigar_len=0;
87	uint8_t* prev_bdata=NULL;
88	if (b->data_len>doff) {
89	//cigar string already allocated, replace it
90	int d=b->core.l_qname + b->core.n_cigar * 4;//offset of after-cigar data
91	after_cigar=b->data+d;
92	after_cigar_len=b->data_len-d;
93	}
94	const char *s;
95	char *t;
96	int i, op;
97	long x;
98	b->core.n_cigar = 0;
99	if (cigar != NULL && strcmp(cigar, "*") != 0) {
100	for (s = cigar; *s; ++s) {
101	if (isalpha(*s)) b->core.n_cigar++;
102	else if (!isdigit(*s)) {
103	GError("Error: invalid CIGAR character (%s)\n",cigar);
104	}
105	}
106	if (after_cigar_len>0) { //replace/insert into existing full data
107	prev_bdata=dupalloc_bdata(b, doff + b->core.n_cigar * 4 + after_cigar_len);
108	memcpy((void)(b->data+doff+b->core.n_cigar4),(void*)after_cigar, after_cigar_len);
109	free(prev_bdata);
110	}
111	else {
112	realloc_bdata(b, doff + b->core.n_cigar * 4);
113	}
114	for (i = 0, s = cigar; i != b->core.n_cigar; ++i) {
115	x = strtol(s, &t, 10);
116	op = toupper(*t);
117	if (op == 'M' \|\| op == '=' \|\| op == 'X') op = BAM_CMATCH;
118	else if (op == 'I') op = BAM_CINS;
119	else if (op == 'D') op = BAM_CDEL;
120	else if (op == 'N') op = BAM_CREF_SKIP;
121	else if (op == 'S') op = BAM_CSOFT_CLIP;
122	else if (op == 'H') op = BAM_CHARD_CLIP;
123	else if (op == 'P') op = BAM_CPAD;
124	else GError("Error: invalid CIGAR operation (%s)\n",cigar);
125	s = t + 1;
126	bam1_cigar(b)[i] = x << BAM_CIGAR_SHIFT \| op;
127	}
128	if (*s) GError("Error: unmatched CIGAR operation (%s)\n",cigar);
129	b->core.bin = bam_reg2bin(b->core.pos, bam_calend(&b->core, bam1_cigar(b)));
130	} else {//no CIGAR string given
131	if (!(b->core.flag&BAM_FUNMAP)) {
132	GMessage("Warning: mapped sequence without CIGAR (%s)\n", (char*)b->data);
133	b->core.flag \|= BAM_FUNMAP;
134	}
135	b->core.bin = bam_reg2bin(b->core.pos, b->core.pos + 1);
136	}
137	setupCoordinates();
138	} //set_cigar()
139
140	void GBamRecord::add_sequence(const char* qseq, int slen) {
141	//must be called AFTER set_cigar (cannot replace existing sequence for now)
142	if (qseq==NULL) return; //should we ever care about this?
143	if (slen<0) slen=strlen(qseq);
144	int doff = b->core.l_qname + b->core.n_cigar * 4;
145	if (strcmp(qseq, "*")!=0) {
146	b->core.l_qseq=slen;
147	if (b->core.n_cigar && b->core.l_qseq != (int32_t)bam_cigar2qlen(&b->core, bam1_cigar(b)))
148	GError("Error: CIGAR and sequence length are inconsistent!(%s)\n",
149	qseq);
150	uint8_t* p = (uint8_t*)realloc_bdata(b, doff + (b->core.l_qseq+1)/2 + b->core.l_qseq) + doff;
151	//also allocated quals memory
152	memset(p, 0, (b->core.l_qseq+1)/2);
153	for (int i = 0; i < b->core.l_qseq; ++i)
154	p[i/2] \|= bam_nt16_table[(int)qseq[i]] << 4*(1-i%2);
155	} else b->core.l_qseq = 0;
156	}
157
158	void GBamRecord::add_quals(const char* quals) {
159	//requires core.l_qseq already set
160	//and must be called AFTER add_sequence(), which also allocates the memory for quals
161	uint8_t* p = b->data+(b->core.l_qname + b->core.n_cigar * 4 + (b->core.l_qseq+1)/2);
162	if (quals==NULL \|\| strcmp(quals, "*") == 0) {
163	for (int i=0;i < b->core.l_qseq; i++) p[i] = 0xff;
164	return;
165	}
166	for (int i=0;i < b->core.l_qseq; i++) p[i] = quals[i]-33;
167	}
168
169	void GBamRecord::add_aux(const char* str) {
170	//requires: being called AFTER add_quals()
171	static char tag[2];
172	static uint8_t abuf[512];
173	//requires: being called AFTER add_quals()
174	int strl=strlen(str);
175	//int doff = b->core.l_qname + b->core.n_cigar*4 + (b->core.l_qseq+1)/2 + b->core.l_qseq + b->l_aux;
176	//int doff0=doff;
177	if (strl < 6 \|\| str[2] != ':' \|\| str[4] != ':')
178	parse_error("missing colon in auxiliary data");
179	tag[0] = str[0]; tag[1] = str[1];
180	uint8_t atype = str[3];
181	uint8_t* adata=abuf;
182	int alen=0;
183	if (atype == 'A' \|\| atype == 'a' \|\| atype == 'c' \|\| atype == 'C') { // c and C for backward compatibility
184	atype='A';
185	alen=1;
186	adata=(uint8_t*)&str[5];
187	}
188	else if (atype == 'I' \|\| atype == 'i') {
189	long long x=(long long)atoll(str + 5);
190	if (x < 0) {
191	if (x >= -127) {
192	atype='c';
193	abuf[0] = (int8_t)x;
194	alen=1;
195	}
196	else if (x >= -32767) {
197	atype = 's';
198	(int16_t)abuf = (int16_t)x;
199	alen=2;
200	}
201	else {
202	atype='i';
203	(int32_t)abuf = (int32_t)x;
204	alen=4;
205	if (x < -2147483648ll)
206	GMessage("Parse warning: integer %lld is out of range.", x);
207	}
208	} else { //x >=0
209	if (x <= 255) {
210	atype = 'C';
211	abuf[0] = (uint8_t)x;
212	alen=1;
213	}
214	else if (x <= 65535) {
215	atype='S';
216	(uint16_t)abuf = (uint16_t)x;
217	alen=2;
218	}
219	else {
220	atype='I';
221	(uint32_t)abuf = (uint32_t)x;
222	alen=4;
223	if (x > 4294967295ll)
224	GMessage("Parse warning: integer %lld is out of range.", x);
225	}
226	}
227	} //integer type
228	else if (atype == 'f') {
229	(float)abuf = (float)atof(str + 5);
230	alen = sizeof(float);
231	}
232	else if (atype == 'd') { //?
233	(float)abuf = (float)atof(str + 9);
234	alen=8;
235	}
236	else if (atype == 'Z' \|\| atype == 'H') {
237	if (atype == 'H') { // check whether the hex string is valid
238	if ((strl - 5) % 2 == 1) parse_error("length of the hex string not even");
239	for (int i = 0; i < strl - 5; ++i) {
240	int c = toupper(str[5 + i]);
241	if (!((c >= '0' && c <= '9') \|\| (c >= 'A' && c <= 'F')))
242	parse_error("invalid hex character");
243	}
244	}
245	memcpy(abuf, str + 5, strl - 5);
246	abuf[strl-5] = 0;
247	alen=strl-4;
248	} else parse_error("unrecognized aux type");
249	this->add_aux(tag, atype, alen, adata);
250	}//add_aux()
251
252
253	void GBamRecord::setupCoordinates() {
254	uint32_t *cigar = bam1_cigar(b);
255	const bam1_core_t *c = &b->core;
256	if (c->flag & BAM_FUNMAP) return; /* skip unmapped reads */
257	int l=0;
258	start=c->pos+1;
259	int exstart=c->pos;
260	for (int i = 0; i < c->n_cigar; ++i) {
261	int op = cigar[i]&0xf;
262	if (op == BAM_CMATCH \|\| op==BAM_CEQUAL \|\|
263	op == BAM_CDIFF \|\| op == BAM_CDEL) {
264	l += cigar[i]>>4;
265	}
266	else if (op == BAM_CREF_SKIP) { //N
267	//intron starts
268	//exon ends here
269	GSeg exon(exstart+1,c->pos+l);
270	exons.Add(exon);
271	l += cigar[i]>>4;
272	exstart=c->pos+l;
273	}
274	}
275	GSeg exon(exstart+1,c->pos+l);
276	exons.Add(exon);
277	end=c->pos+l;
278	}
279
280	int GBamRecord::find_tag(const char tag[2], uint8_t* & s, char& tag_type) {
281	//position s at the beginning of tag "data" (after the type char)
282	//returns the length of tag data, and tag type in tag_type
283	s=bam1_aux(b);
284	while (s < b->data + b->data_len) {
285	char key[2];
286	key[0] = (char)s[0]; key[1] = (char)s[1];
287	s += 2; tag_type = (char)*s; ++s;
288	int inc=0;
289	int m_inc=0; //for 'B' case
290	uint8_t sub_type=0; // --,,--
291	switch (tag_type) {
292	case 'A':
293	case 'C':
294	case 'c':
295	inc=1;
296	break;
297	case 'S':
298	case 's':
299	inc=2;
300	break;
301	case 'I':
302	case 'i':
303	case 'f':
304	inc=4;
305	break;
306	case 'd':
307	inc=8;
308	break;
309	case 'B':
310	sub_type = *(s+1);
311	int32_t n;
312	memcpy(&n, s+1, 4);
313	inc += 5;
314	//kputc(type, &str); kputc(':', &str); kputc(sub_type, &str);
315	m_inc=0;
316	if (sub_type == 'c' \|\| sub_type == 'C')
317	{ m_inc=1; }
318	else if (sub_type == 's' \|\| sub_type == 'S')
319	{ m_inc = 2; }
320	else if ('i' == sub_type \|\| 'I' == sub_type \|\| 'f' == sub_type)
321	{ m_inc = 4; }
322	if (m_inc==0) GError("Error: invalid 'B' array subtype (%c)!\n",sub_type);
323	inc += m_inc*n;
324	break;
325	case 'H':
326	case 'Z':
327	while (*(s+inc)) ++inc;
328	break;
329	} //switch (tag_type)
330	if (tag[0]==key[0] && tag[1]==key[1])
331	return inc;
332	s+=inc;
333	}//while aux data
334	return 0;
335	}
336
337	char GBamRecord::tag_char(const char tag[2]) { //retrieve tag data as single char
338	uint8_t *s;
339	char tag_type=0;
340	int vlen=find_tag(tag, s, tag_type);
341	if (vlen==0) return 0;
342	//if (vlen>1) GWarning("Warning: tag %c%c value has length %d, but char was expected.\n",
343	// tag[0],tag[1],vlen);
344	return (char)s[0];
345	}
346
347	int GBamRecord::tag_int(const char tag[2]) { //get the numeric value of tag
348	uint8_t *s;
349	char tag_type=0;
350	int vlen=find_tag(tag, s, tag_type);
351	if (vlen==0) return 0;
352	if (vlen==1) return (int)((int8_t)s);
353	else if (vlen==2) return (int)((int16_t)s);
354	else if (vlen==4) return (int)((int32_t)s);
355	else GMessage("Warning: tag %c%c value has length %d, but int type was expected.\n",
356	tag[0],tag[1], vlen);
357	return 0;
358	}
359
360	char* GBamRecord::tag_str(const char tag[2]) { //return string value for a tag
361	uint8_t *s;
362	char tag_type=0;
363	int vlen=find_tag(tag, s, tag_type);
364	if (vlen==0) return NULL; //not found
365	//if (vlen>1) GWarning("Warning: tag %c%c value has length %d, but char was expected.\n",
366	// tag[0],tag[1],vlen);
367	return (char *)s;
368	}
369
370	char GBamRecord::spliceStrand() { // '+', '-' from the XS tag, or 0 if no XS tag
371	uint8_t *s;
372	char tag_type=0;
373	int vlen=find_tag("XS", s, tag_type);
374	if (vlen==0) return '.';
375	return (char)s[0];
376	}
377
378	char* GBamRecord::sequence() { //user must free this after use
379	char s = (char)bam1_seq(b);
380	char* qseq=NULL;
381	GMALLOC(qseq, (b->core.l_qseq+1));
382	int i;
383	for (i=0;i<(b->core.l_qseq);i++) {
384	int8_t v = bam1_seqi(s,i);
385	qseq[i] = bam_nt16_rev_table[v];
386	}
387	qseq[i] = 0;
388	return qseq;
389	}
390
391	char* GBamRecord::qualities() {//user must free this after use
392	char qual = (char)bam1_qual(b);
393	char* qv=NULL;
394	GMALLOC(qv, (b->core.l_qseq+1) );
395	int i;
396	for(i=0;i<(b->core.l_qseq);i++) {
397	qv[i]=qual[i]+33;
398	}
399	qv[i]=0;
400	return qv;
401	}
402
403	char* GBamRecord::cigar() { //returns text version of the CIGAR string; must be freed by user
404	kstring_t str;
405	str.l = str.m = 0; str.s = 0;
406	if (b->core.n_cigar == 0) kputc('*', &str);
407	else {
408	for (int i = 0; i < b->core.n_cigar; ++i) {
409	kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
410	kputc("MIDNSHP=X"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
411	}
412	}
413	return str.s;
414	}