static int populate_merged_header(bam_hdr_t *hdr, merged_header_t *merged_hdr) {
trans_tbl_t dummy;
int res;
res = trans_tbl_init(merged_hdr, hdr, &dummy, 0, 0, 1, NULL);
trans_tbl_destroy(&dummy);
return res;
}
int samtools_test_trans_tbl_init_main(int argc, char**argv)
{
const int NUM_TESTS = 6;
int verbose = 0;
int success = 0;
int failure = 0;
int getopt_char;
while ((getopt_char = getopt(argc, argv, "v")) != -1) {
switch (getopt_char) {
case 'v':
++verbose;
break;
default:
break;
}
}
// Set the seed to a fixed value so that calls to lrand48 within functions return predictable values
const long GIMMICK_SEED = 0x1234330e;
srand48(GIMMICK_SEED);
bam_hdr_t* out;
bam_hdr_t* translate;
if (verbose) fprintf(pysam_stdout, "BEGIN test 1\n");
// setup
trans_tbl_t tbl_1;
merged_header_t *merged_hdr = init_merged_header();
translate = setup_test_1(merged_hdr);
assert(translate);
// test
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
}
if (verbose) fprintf(pysam_stdout, "RUN test 1\n");
trans_tbl_init(merged_hdr, translate, &tbl_1, false, false, true, NULL);
out = finish_merged_header(merged_hdr);
free_merged_header(merged_hdr);
if (verbose) fprintf(pysam_stdout, "END RUN test 1\n");
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
fprintf(pysam_stdout, "out\n");
dump_header(out);
}
if (check_test_1(translate, out, &tbl_1)) {
if (verbose) fprintf(pysam_stdout, "Test 1 : PASS\n");
++success;
} else {
if (verbose) fprintf(pysam_stdout, "Test 1 : FAIL\n");
fprintf(pysam_stderr, "Test 1 : FAIL\n");
++failure;
}
// teardown
bam_hdr_destroy(translate);
bam_hdr_destroy(out);
trans_tbl_destroy(&tbl_1);
if (verbose) fprintf(pysam_stdout, "END test 1\n");
// test
if (verbose) fprintf(pysam_stdout, "BEGIN test 2\n");
// reinit
trans_tbl_t tbl_2;
merged_hdr = init_merged_header();
translate = setup_test_2(merged_hdr);
assert(translate);
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
}
if (verbose) fprintf(pysam_stdout, "RUN test 2\n");
trans_tbl_init(merged_hdr, translate, &tbl_2, false, false, true, NULL);
out = finish_merged_header(merged_hdr);
free_merged_header(merged_hdr);
if (verbose) fprintf(pysam_stdout, "END RUN test 2\n");
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
fprintf(pysam_stdout, "out\n");
dump_header(out);
}
if (check_test_2(translate, out, &tbl_2)) {
if (verbose) fprintf(pysam_stdout, "Test 2 : PASS\n");
++success;
} else {
if (verbose) fprintf(pysam_stdout, "Test 2 : FAIL\n");
fprintf(pysam_stderr, "Test 2 : FAIL\n");
++failure;
}
// teardown
bam_hdr_destroy(translate);
bam_hdr_destroy(out);
trans_tbl_destroy(&tbl_2);
if (verbose) fprintf(pysam_stdout, "END test 2\n");
// test
if (verbose) fprintf(pysam_stdout, "BEGIN test 3\n");
// reinit
trans_tbl_t tbl_3;
merged_hdr = init_merged_header();
translate = setup_test_3(merged_hdr);
assert(translate);
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
}
if (verbose) fprintf(pysam_stdout, "RUN test 3\n");
trans_tbl_init(merged_hdr, translate, &tbl_3, false, false, true, NULL);
out = finish_merged_header(merged_hdr);
free_merged_header(merged_hdr);
if (verbose) fprintf(pysam_stdout, "END RUN test 3\n");
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
fprintf(pysam_stdout, "out\n");
dump_header(out);
}
if (check_test_3(translate, out, &tbl_3)) {
if (verbose) fprintf(pysam_stdout, "Test 3 : PASS\n");
++success;
} else {
if (verbose) fprintf(pysam_stdout, "Test 3 : FAIL\n");
fprintf(pysam_stderr, "Test 3 : FAIL\n");
++failure;
}
// teardown
bam_hdr_destroy(translate);
bam_hdr_destroy(out);
trans_tbl_destroy(&tbl_3);
if (verbose) fprintf(pysam_stdout, "END test 3\n");
// test
if (verbose) fprintf(pysam_stdout, "BEGIN test 4\n");
// reinit
trans_tbl_t tbl_4;
merged_hdr = init_merged_header();
translate = setup_test_4(merged_hdr);
assert(translate);
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
}
if (verbose) fprintf(pysam_stdout, "RUN test 4\n");
trans_tbl_init(merged_hdr, translate, &tbl_4, false, false, true, NULL);
out = finish_merged_header(merged_hdr);
free_merged_header(merged_hdr);
if (verbose) fprintf(pysam_stdout, "END RUN test 4\n");
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
fprintf(pysam_stdout, "out\n");
dump_header(out);
}
if (check_test_4(translate, out, &tbl_4)) {
if (verbose) fprintf(pysam_stdout, "Test 4 : PASS\n");
++success;
} else {
if (verbose) fprintf(pysam_stdout, "Test 4 : FAIL\n");
fprintf(pysam_stderr, "Test 4 : FAIL\n");
++failure;
}
// teardown
bam_hdr_destroy(translate);
bam_hdr_destroy(out);
trans_tbl_destroy(&tbl_4);
if (verbose) fprintf(pysam_stdout, "END test 4\n");
// test
if (verbose) fprintf(pysam_stdout, "BEGIN test 5\n");
// reinit
trans_tbl_t tbl_5;
merged_hdr = init_merged_header();
translate = setup_test_5(merged_hdr);
assert(translate);
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
}
if (verbose) fprintf(pysam_stdout, "RUN test 5\n");
trans_tbl_init(merged_hdr, translate, &tbl_5, false, false, true, NULL);
out = finish_merged_header(merged_hdr);
free_merged_header(merged_hdr);
if (verbose) fprintf(pysam_stdout, "END RUN test 5\n");
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
fprintf(pysam_stdout, "out\n");
dump_header(out);
}
if (check_test_5(translate, out, &tbl_5)) {
if (verbose) fprintf(pysam_stdout, "Test 5 : PASS\n");
++success;
} else {
if (verbose) fprintf(pysam_stdout, "Test 5 : FAIL\n");
fprintf(pysam_stderr, "Test 5 : FAIL\n");
++failure;
}
// teardown
bam_hdr_destroy(translate);
bam_hdr_destroy(out);
trans_tbl_destroy(&tbl_5);
if (verbose) fprintf(pysam_stdout, "END test 5\n");
// test
if (verbose) fprintf(pysam_stdout, "BEGIN test 6\n");
// reinit
trans_tbl_t tbl_6;
merged_hdr = init_merged_header();
translate = setup_test_6(merged_hdr);
assert(translate);
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
}
if (verbose) fprintf(pysam_stdout, "RUN test 6\n");
trans_tbl_init(merged_hdr, translate, &tbl_6, false, false, true, "filename");
out = finish_merged_header(merged_hdr);
free_merged_header(merged_hdr);
if (verbose) fprintf(pysam_stdout, "END RUN test 6\n");
if (verbose > 1) {
fprintf(pysam_stdout, "translate\n");
dump_header(translate);
fprintf(pysam_stdout, "out\n");
dump_header(out);
}
if (check_test_6(translate, out, &tbl_6)) {
if (verbose) fprintf(pysam_stdout, "Test 6 : PASS\n");
++success;
} else {
if (verbose) fprintf(pysam_stdout, "Test 6 : FAIL\n");
fprintf(pysam_stderr, "Test 6 : FAIL\n");
++failure;
}
// teardown
bam_hdr_destroy(translate);
bam_hdr_destroy(out);
trans_tbl_destroy(&tbl_6);
if (verbose) fprintf(pysam_stdout, "END test 6\n");
if (success == NUM_TESTS) {
return 0;
} else {
fprintf(pysam_stderr, "%d failures %d successes\n", failure, success);
return 1;
}
}
/*!
@abstract Merge multiple sorted BAM.
@param is_by_qname whether to sort by query name
@param out output BAM file name
@param mode sam_open() mode to be used to create the final output file
(overrides level settings from UNCOMP and LEVEL1 flags)
@param headers name of SAM file from which to copy '@' header lines,
or NULL to copy them from the first file to be merged
@param n number of files to be merged
@param fn names of files to be merged
@param flag flags that control how the merge is undertaken
@param reg region to merge
@param n_threads number of threads to use (passed to htslib)
@discussion Padding information may NOT correctly maintained. This
function is NOT thread safe.
*/
int bam_merge_core2(int by_qname, const char *out, const char *mode, const char *headers, int n, char * const *fn, int flag, const char *reg, int n_threads)
{
samFile *fpout, **fp;
heap1_t *heap;
bam_hdr_t *hout = NULL;
int i, j, *RG_len = NULL;
uint64_t idx = 0;
char **RG = NULL;
hts_itr_t **iter = NULL;
bam_hdr_t **hdr = NULL;
trans_tbl_t *translation_tbl = NULL;
// Is there a specified pre-prepared header to use for output?
if (headers) {
samFile* fpheaders = sam_open(headers, "r");
if (fpheaders == NULL) {
const char *message = strerror(errno);
fprintf(pysamerr, "[bam_merge_core] cannot open '%s': %s\n", headers, message);
return -1;
}
hout = sam_hdr_read(fpheaders);
sam_close(fpheaders);
}
g_is_by_qname = by_qname;
fp = (samFile**)calloc(n, sizeof(samFile*));
heap = (heap1_t*)calloc(n, sizeof(heap1_t));
iter = (hts_itr_t**)calloc(n, sizeof(hts_itr_t*));
hdr = (bam_hdr_t**)calloc(n, sizeof(bam_hdr_t*));
translation_tbl = (trans_tbl_t*)calloc(n, sizeof(trans_tbl_t));
// prepare RG tag from file names
if (flag & MERGE_RG) {
RG = (char**)calloc(n, sizeof(char*));
RG_len = (int*)calloc(n, sizeof(int));
for (i = 0; i != n; ++i) {
int l = strlen(fn[i]);
const char *s = fn[i];
if (l > 4 && strcmp(s + l - 4, ".bam") == 0) l -= 4;
for (j = l - 1; j >= 0; --j) if (s[j] == '/') break;
++j; l -= j;
RG[i] = (char*)calloc(l + 1, 1);
RG_len[i] = l;
strncpy(RG[i], s + j, l);
}
}
// open and read the header from each file
for (i = 0; i < n; ++i) {
bam_hdr_t *hin;
fp[i] = sam_open(fn[i], "r");
if (fp[i] == NULL) {
int j;
fprintf(pysamerr, "[bam_merge_core] fail to open file %s\n", fn[i]);
for (j = 0; j < i; ++j) sam_close(fp[j]);
free(fp); free(heap);
// FIXME: possible memory leak
return -1;
}
hin = sam_hdr_read(fp[i]);
if (hout)
trans_tbl_init(hout, hin, translation_tbl+i, flag & MERGE_COMBINE_RG, flag & MERGE_COMBINE_PG);
else {
// As yet, no headers to merge into...
hout = bam_hdr_dup(hin);
// ...so no need to translate header into itself
trans_tbl_init(hout, hin, translation_tbl+i, true, true);
}
// TODO sam_itr_next() doesn't yet work for SAM files,
// so for those keep the headers around for use with sam_read1()
if (hts_get_format(fp[i])->format == sam) hdr[i] = hin;
else { bam_hdr_destroy(hin); hdr[i] = NULL; }
if ((translation_tbl+i)->lost_coord_sort && !by_qname) {
fprintf(pysamerr, "[bam_merge_core] Order of targets in file %s caused coordinate sort to be lost\n", fn[i]);
}
}
// Transform the header into standard form
pretty_header(&hout->text,hout->l_text);
// If we're only merging a specified region move our iters to start at that point
if (reg) {
int* rtrans = rtrans_build(n, hout->n_targets, translation_tbl);
int tid, beg, end;
const char *name_lim = hts_parse_reg(reg, &beg, &end);
char *name = malloc(name_lim - reg + 1);
memcpy(name, reg, name_lim - reg);
name[name_lim - reg] = '\0';
tid = bam_name2id(hout, name);
free(name);
if (tid < 0) {
fprintf(pysamerr, "[%s] Malformated region string or undefined reference name\n", __func__);
return -1;
}
for (i = 0; i < n; ++i) {
hts_idx_t *idx = sam_index_load(fp[i], fn[i]);
// (rtrans[i*n+tid]) Look up what hout tid translates to in input tid space
int mapped_tid = rtrans[i*hout->n_targets+tid];
if (mapped_tid != INT32_MIN) {
iter[i] = sam_itr_queryi(idx, mapped_tid, beg, end);
} else {
iter[i] = sam_itr_queryi(idx, HTS_IDX_NONE, 0, 0);
}
hts_idx_destroy(idx);
if (iter[i] == NULL) break;
}
free(rtrans);
} else {
for (i = 0; i < n; ++i) {
if (hdr[i] == NULL) {
iter[i] = sam_itr_queryi(NULL, HTS_IDX_REST, 0, 0);
if (iter[i] == NULL) break;
}
else iter[i] = NULL;
}
}
if (i < n) {
fprintf(pysamerr, "[%s] Memory allocation failed\n", __func__);
return -1;
}
// Load the first read from each file into the heap
for (i = 0; i < n; ++i) {
heap1_t *h = heap + i;
h->i = i;
h->b = bam_init1();
if ((iter[i]? sam_itr_next(fp[i], iter[i], h->b) : sam_read1(fp[i], hdr[i], h->b)) >= 0) {
bam_translate(h->b, translation_tbl + i);
h->pos = ((uint64_t)h->b->core.tid<<32) | (uint32_t)((int32_t)h->b->core.pos+1)<<1 | bam_is_rev(h->b);
h->idx = idx++;
}
else {
h->pos = HEAP_EMPTY;
bam_destroy1(h->b);
h->b = NULL;
}
}
// Open output file and write header
if ((fpout = sam_open(out, mode)) == 0) {
fprintf(pysamerr, "[%s] fail to create the output file.\n", __func__);
return -1;
}
sam_hdr_write(fpout, hout);
if (!(flag & MERGE_UNCOMP)) hts_set_threads(fpout, n_threads);
// Begin the actual merge
ks_heapmake(heap, n, heap);
while (heap->pos != HEAP_EMPTY) {
bam1_t *b = heap->b;
if (flag & MERGE_RG) {
uint8_t *rg = bam_aux_get(b, "RG");
if (rg) bam_aux_del(b, rg);
bam_aux_append(b, "RG", 'Z', RG_len[heap->i] + 1, (uint8_t*)RG[heap->i]);
}
sam_write1(fpout, hout, b);
if ((j = (iter[heap->i]? sam_itr_next(fp[heap->i], iter[heap->i], b) : sam_read1(fp[heap->i], hdr[heap->i], b))) >= 0) {
bam_translate(b, translation_tbl + heap->i);
heap->pos = ((uint64_t)b->core.tid<<32) | (uint32_t)((int)b->core.pos+1)<<1 | bam_is_rev(b);
heap->idx = idx++;
} else if (j == -1) {
heap->pos = HEAP_EMPTY;
bam_destroy1(heap->b);
heap->b = NULL;
} else fprintf(pysamerr, "[bam_merge_core] '%s' is truncated. Continue anyway.\n", fn[heap->i]);
ks_heapadjust(heap, 0, n, heap);
}
// Clean up and close
if (flag & MERGE_RG) {
for (i = 0; i != n; ++i) free(RG[i]);
free(RG); free(RG_len);
}
for (i = 0; i < n; ++i) {
trans_tbl_destroy(translation_tbl + i);
hts_itr_destroy(iter[i]);
bam_hdr_destroy(hdr[i]);
sam_close(fp[i]);
}
bam_hdr_destroy(hout);
sam_close(fpout);
free(translation_tbl); free(fp); free(heap); free(iter); free(hdr);
return 0;
}