inline int32_t left() const {
if (isPaired()) {
return std::min(bam_pos(read1), bam_pos(read2));
} else {
return bam_pos(read1);
}
}
inline int32_t right() const {
if (isPaired()) {
return std::max(bam_pos(read1) + bam_seq_len(read1),
bam_pos(read2) + bam_seq_len(read2));
} else {
return bam_pos(read1) + bam_seq_len(read1);
}
}
inline uint32_t fragLen() const {
if (!isPaired()) { return 0; }
auto leftmost1 = bam_pos(read1);
auto leftmost2 = bam_pos(read2);
// The length of the mapped read that is "rightmost" w.r.t. the forward strand.
auto rightmostLen = (leftmost1 < leftmost2) ? bam_seq_len(read2) : bam_seq_len(read1);
return std::abs(leftmost1 - leftmost2) + rightmostLen;
//return std::abs(read1->core.isize) + std::abs(read1->core.l_qseq) + std::abs(read2->core.l_qseq);
}
int main(int argc, char **argv) {
scram_fd **in, *out;
int n_input, i;
bam_seq_t **s;
char imode[10], *in_f = "", omode[10], *out_f = "";
int level = '\0'; // nul terminate string => auto level
int c, verbose = 0;
int s_opt = 0, S_opt = 0, embed_ref = 0;
char *ref_fn = NULL;
int start, end;
char ref_name[1024] = {0};
refs_t *refs = NULL;
/* Parse command line arguments */
while ((c = getopt(argc, argv, "u0123456789hvs:S:V:r:XI:O:R:")) != -1) {
switch (c) {
case '0': case '1': case '2': case '3': case '4':
case '5': case '6': case '7': case '8': case '9':
level = c;
break;
case 'u':
level = '0';
break;
case 'h':
usage(stdout);
return 0;
case 'v':
verbose++;
break;
case 's':
s_opt = atoi(optarg);
break;
case 'S':
S_opt = atoi(optarg);
break;
case 'V':
cram_set_option(NULL, CRAM_OPT_VERSION, optarg);
break;
case 'r':
ref_fn = optarg;
break;
case 'X':
embed_ref = 1;
break;
case 'I':
in_f = parse_format(optarg);
break;
case 'O':
out_f = parse_format(optarg);
break;
case 'R': {
char *cp = strchr(optarg, ':');
if (cp) {
*cp = 0;
switch (sscanf(cp+1, "%d-%d", &start, &end)) {
case 1:
end = start;
break;
case 2:
break;
default:
fprintf(stderr, "Malformed range format\n");
return 1;
}
} else {
start = INT_MIN;
end = INT_MAX;
}
strncpy(ref_name, optarg, 1023);
break;
}
case '?':
fprintf(stderr, "Unrecognised option: -%c\n", optopt);
usage(stderr);
return 1;
}
}
/* Open output file */
sprintf(omode, "w%s%c", out_f, level);
if (!(out = scram_open("-", omode))) {
fprintf(stderr, "Failed to open bam file %s\n", argv[optind+1]);
return 1;
}
/* Open multiple input files */
sprintf(imode, "r%s%c", in_f, level);
n_input = argc - optind;
if (!n_input) {
fprintf(stderr, "No input files specified.\n");
return 1;
}
if (!(in = malloc(n_input * sizeof(*in))))
return 1;
if (!(s = malloc(n_input * sizeof(*s))))
return 1;
for (i = 0; i < n_input; i++, optind++) {
s[i] = NULL;
if (*in_f == 0)
sprintf(imode, "r%s%c", detect_format(argv[optind]), level);
if (!(in[i] = scram_open(argv[optind], imode))) {
fprintf(stderr, "Failed to open bam file %s\n", argv[optind]);
return 1;
}
if (i && !hdr_compare(scram_get_header(in[0]),
scram_get_header(in[i]))) {
fprintf(stderr, "Incompatible reference sequence list.\n");
fprintf(stderr, "Currently the @SQ lines need to be identical"
" in all files.\n");
return 1;
}
if (!refs && scram_get_refs(in[i]))
refs = scram_get_refs(in[i]);
if (refs && scram_set_option(in[i], CRAM_OPT_SHARED_REF, refs))
return 1;
}
/* Set any format specific options */
if (refs)
scram_set_option(out, CRAM_OPT_SHARED_REF, refs);
if (scram_set_option(out, CRAM_OPT_VERBOSITY, verbose))
return 1;
if (s_opt)
if (scram_set_option(out, CRAM_OPT_SEQS_PER_SLICE, s_opt))
return 1;
if (S_opt)
if (scram_set_option(out, CRAM_OPT_SLICES_PER_CONTAINER, S_opt))
return 1;
if (embed_ref)
if (scram_set_option(out, CRAM_OPT_EMBED_REF, embed_ref))
return 1;
/* Copy header and refs from in to out, for writing purposes */
// FIXME: do proper merging of @PG lines
// FIXME: track mapping of old PG aux name to new PG aux name per seq
scram_set_header(out, sam_hdr_dup(scram_get_header(in[0])));
// Needs doing after loading the header.
if (ref_fn)
if (scram_set_option(out, CRAM_OPT_REFERENCE, ref_fn))
return 1;
if (scram_get_header(in[0])) {
if (scram_write_header(out))
return 1;
}
/* Do the actual file format conversion */
fprintf(stderr, "Opening and loading initial seqs\n");
for (i = 0; i < n_input; i++) {
if (scram_get_seq(in[i], &s[i]) < 0) {
if (scram_close(in[i]))
return 1;
in[i] = NULL;
free(s[i]);
continue;
}
}
fprintf(stderr, "Merging...\n");
for (;;) {
int64_t best_val = INT64_MAX;
int best_j = 0, j;
for (j = 0; j < n_input; j++) {
bam_seq_t *b = s[j];
uint64_t x;
if (!in[j])
continue;
x = (((uint64_t)bam_ref(b))<<33)
| (bam_pos(b)<<2)
| (bam_strand(b)<<1)
| !(bam_flag(b) & BAM_FREAD1);
if (best_val > x) {
best_val = x;
best_j = j;
}
}
if (best_val == INT64_MAX) { // all closed
break;
}
if (-1 == scram_put_seq(out, s[best_j]))
return 1;
if (scram_get_seq(in[best_j], &s[best_j]) < 0) {
if (scram_close(in[best_j]))
return 1;
in[best_j] = NULL;
free(s[best_j]);
}
}
for (i = 0; i < n_input; i++) {
if (!in[i])
continue;
scram_close(in[i]);
if (s[i])
free(s[i]);
}
/* Finally tidy up and close files */
if (scram_close(out))
return 1;
free(in);
free(s);
return 0;
}
inline int32_t left() { return bam_pos(read); }