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sam.c

#include <string.h>
#include <unistd.h>
#include "faidx.h"
#include "sam.h"

#define TYPE_BAM  1
#define TYPE_READ 2

bam_header_t *bam_header_dup(const bam_header_t *h0)
{
      bam_header_t *h;
      int i;
      h = bam_header_init();
      *h = *h0;
      h->hash = h->dict = h->rg2lib = 0;
      h->text = (char*)calloc(h->l_text + 1, 1);
      memcpy(h->text, h0->text, h->l_text);
      h->target_len = (uint32_t*)calloc(h->n_targets, 4);
      h->target_name = (char**)calloc(h->n_targets, sizeof(void*));
      for (i = 0; i < h->n_targets; ++i) {
            h->target_len[i] = h0->target_len[i];
            h->target_name[i] = strdup(h0->target_name[i]);
      }
      return h;
}
static void append_header_text(bam_header_t *header, char* text, int len)
{
      int x = header->l_text + 1;
      int y = header->l_text + len + 1; // 1 byte null
      if (text == 0) return;
      kroundup32(x); 
      kroundup32(y);
      if (x < y) header->text = (char*)realloc(header->text, y);
      strncpy(header->text + header->l_text, text, len); // we cannot use strcpy() here.
      header->l_text += len;
      header->text[header->l_text] = 0;
}

samfile_t *samopen(const char *fn, const char *mode, const void *aux)
{
      samfile_t *fp;
      fp = (samfile_t*)calloc(1, sizeof(samfile_t));
      if (mode[0] == 'r') { // read
            fp->type |= TYPE_READ;
            if (mode[1] == 'b') { // binary
                  fp->type |= TYPE_BAM;
                  fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r");
                  if (fp->x.bam == 0) goto open_err_ret;
                  fp->header = bam_header_read(fp->x.bam);
            } else { // text
                  fp->x.tamr = sam_open(fn);
                  if (fp->x.tamr == 0) goto open_err_ret;
                  fp->header = sam_header_read(fp->x.tamr);
                  if (fp->header->n_targets == 0) { // no @SQ fields
                        if (aux) { // check if aux is present
                              bam_header_t *textheader = fp->header;
                              fp->header = sam_header_read2((const char*)aux);
                              if (fp->header == 0) goto open_err_ret;
                              append_header_text(fp->header, textheader->text, textheader->l_text);
                              bam_header_destroy(textheader);
                        }
                        if (fp->header->n_targets == 0)
                              fprintf(stderr, "[samopen] no @SQ lines in the header.\n");
                  } else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets);
            }
      } else if (mode[0] == 'w') { // write
            fp->header = bam_header_dup((const bam_header_t*)aux);
            if (mode[1] == 'b') { // binary
                  char bmode[3];
                  bmode[0] = 'w'; bmode[1] = strstr(mode, "u")? 'u' : 0; bmode[2] = 0;
                  fp->type |= TYPE_BAM;
                  fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode);
                  if (fp->x.bam == 0) goto open_err_ret;
                  bam_header_write(fp->x.bam, fp->header);
            } else { // text
                  // open file
                  fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
                  if (fp->x.tamr == 0) goto open_err_ret;
                  if (strstr(mode, "X")) fp->type |= BAM_OFSTR<<2;
                  else if (strstr(mode, "x")) fp->type |= BAM_OFHEX<<2;
                  else fp->type |= BAM_OFDEC<<2;
                  // write header
                  if (strstr(mode, "h")) {
                        int i;
                        bam_header_t *alt;
                        // parse the header text 
                        alt = bam_header_init();
                        alt->l_text = fp->header->l_text; alt->text = fp->header->text;
                        sam_header_parse(alt);
                        alt->l_text = 0; alt->text = 0;
                        // check if there are @SQ lines in the header
                        fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw);
                        if (alt->n_targets) { // then write the header text without dumping ->target_{name,len}
                              if (alt->n_targets != fp->header->n_targets)
                                    fprintf(stderr, "[samopen] inconsistent number of target sequences.\n");
                        } else { // then dump ->target_{name,len}
                              for (i = 0; i < fp->header->n_targets; ++i)
                                    fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]);
                        }
                        bam_header_destroy(alt);
                  }
            }
      }
      return fp;

open_err_ret:
      free(fp);
      return 0;
}

void samclose(samfile_t *fp)
{
      if (fp == 0) return;
      if (fp->header) bam_header_destroy(fp->header);
      if (fp->type & TYPE_BAM) bam_close(fp->x.bam);
      else if (fp->type & TYPE_READ) sam_close(fp->x.tamr);
      else fclose(fp->x.tamw);
      free(fp);
}

int samread(samfile_t *fp, bam1_t *b)
{
      if (fp == 0 || !(fp->type & TYPE_READ)) return -1; // not open for reading
      if (fp->type & TYPE_BAM) return bam_read1(fp->x.bam, b);
      else return sam_read1(fp->x.tamr, fp->header, b);
}

int samwrite(samfile_t *fp, const bam1_t *b)
{
      if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing
      if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b);
      else {
            char *s = bam_format1_core(fp->header, b, fp->type>>2&3);
            int l = strlen(s);
            fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
            free(s);
            return l + 1;
      }
}

int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data)
{
      bam_plbuf_t *buf;
      int ret;
      bam1_t *b;
      b = bam_init1();
      buf = bam_plbuf_init(func, func_data);
      bam_plbuf_set_mask(buf, mask);
      while ((ret = samread(fp, b)) >= 0)
            bam_plbuf_push(b, buf);
      bam_plbuf_push(0, buf);
      bam_plbuf_destroy(buf);
      bam_destroy1(b);
      return 0;
}

char *samfaipath(const char *fn_ref)
{
      char *fn_list = 0;
      if (fn_ref == 0) return 0;
      fn_list = calloc(strlen(fn_ref) + 5, 1);
      strcat(strcpy(fn_list, fn_ref), ".fai");
      if (access(fn_list, R_OK) == -1) { // fn_list is unreadable
            if (access(fn_ref, R_OK) == -1) {
                  fprintf(stderr, "[samfaipath] fail to read file %s.\n", fn_ref);
            } else {
                  fprintf(stderr, "[samfaipath] build FASTA index...\n");
                  if (fai_build(fn_ref) == -1) {
                        fprintf(stderr, "[samfaipath] fail to build FASTA index.\n");
                        free(fn_list); fn_list = 0;
                  }
            }
      }
      return fn_list;
}

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