static int aux_fields1(void)
{
static const char sam[] = "data:"
"@SQ\tSN:one\tLN:1000\n"
"@SQ\tSN:two\tLN:500\n"
"r1\t0\tone\t500\t20\t8M\t*\t0\t0\tATGCATGC\tqqqqqqqq\tXA:A:k\tXi:i:37\tXf:f:" xstr(PI) "\tXd:d:" xstr(E) "\tXZ:Z:" HELLO "\tXH:H:" BEEF "\tXB:B:c,-2,0,+2\tZZ:i:1000000\n";
// Canonical form of the alignment record above, as output by sam_format1()
static const char r1[] = "r1\t0\tone\t500\t20\t8M\t*\t0\t0\tATGCATGC\tqqqqqqqq\tXA:A:k\tXi:i:37\tXf:f:3.14159\tXd:d:2.71828\tXZ:Z:" HELLO "\tXH:H:" BEEF "\tXB:B:c,-2,0,2\tZZ:i:1000000";
samFile *in = sam_open(sam, "r");
bam_hdr_t *header = sam_hdr_read(in);
bam1_t *aln = bam_init1();
uint8_t *p;
uint32_t n;
kstring_t ks = { 0, 0, NULL };
if (sam_read1(in, header, aln) >= 0) {
if ((p = check_bam_aux_get(aln, "XA", 'A')) && bam_aux2A(p) != 'k')
fail("XA field is '%c', expected 'k'", bam_aux2A(p));
if ((p = check_bam_aux_get(aln, "Xi", 'C')) && bam_aux2i(p) != 37)
fail("Xi field is %d, expected 37", bam_aux2i(p));
if ((p = check_bam_aux_get(aln, "Xf", 'f')) && fabs(bam_aux2f(p) - PI) > 1E-6)
fail("Xf field is %.12f, expected pi", bam_aux2f(p));
if ((p = check_bam_aux_get(aln, "Xd", 'd')) && fabs(bam_aux2f(p) - E) > 1E-6)
fail("Xf field is %.12f, expected e", bam_aux2f(p));
if ((p = check_bam_aux_get(aln, "XZ", 'Z')) && strcmp(bam_aux2Z(p), HELLO) != 0)
fail("XZ field is \"%s\", expected \"%s\"", bam_aux2Z(p), HELLO);
if ((p = check_bam_aux_get(aln, "XH", 'H')) && strcmp(bam_aux2Z(p), BEEF) != 0)
fail("XH field is \"%s\", expected \"%s\"", bam_aux2Z(p), BEEF);
// TODO Invent and use bam_aux2B()
if ((p = check_bam_aux_get(aln, "XB", 'B')) && ! (memcmp(p, "Bc", 2) == 0 && (memcpy(&n, p+2, 4), n) == 3 && memcmp(p+6, "\xfe\x00\x02", 3) == 0))
fail("XB field is %c,..., expected c,-2,0,+2", p[1]);
if ((p = check_bam_aux_get(aln, "ZZ", 'I')) && bam_aux2i(p) != 1000000)
fail("ZZ field is %d, expected 1000000", bam_aux2i(p));
if (sam_format1(header, aln, &ks) < 0)
fail("can't format record");
if (strcmp(ks.s, r1) != 0)
fail("record formatted incorrectly: \"%s\"", ks.s);
free(ks.s);
}
else fail("can't read record");
bam_destroy1(aln);
bam_hdr_destroy(header);
sam_close(in);
return 1;
}
int do_grep() {
#ifdef DEBUGa
printf("[!]do_grep\n");
#endif
BamInfo_t *pbam;
kh_cstr_t BamID;
khiter_t ki, bami;
kstring_t ks1 = { 0, 0, NULL };
kstring_t ks2 = { 0, 0, NULL };
kstring_t ks3 = { 0, 0, NULL };
samFile *in;
bam_hdr_t *h;
hts_idx_t *idx;
bam1_t *b, *d, *d2, *bR1, *bR2, *bR3;
bR1 = bam_init1(); bR2 = bam_init1(); bR3 = bam_init1();
//htsFile *out;
//hts_opt *in_opts = NULL, *out_opts = NULL;
int r = 0, exit_code = 0;
kvec_t(bam1_t) R1, R2, RV;
pierCluster_t *pierCluster;
//samdat_t tmp_samdat;
FILE *fs = fopen("./test.txt","w");
for (bami = kh_begin(bamNFOp); bami != kh_end(bamNFOp); ++bami) {
//printf(">[%d]:\n",bami);
if (kh_exist(bamNFOp, bami)) {
kv_init(R1); kv_init(R2); kv_init(RV);
//tmp_samdat = (const samdat_t){ 0 };
//memset(&tmp_samdat,0,sizeof(samdat_t));
//printf("-[%d]:\n",bami);
BamID = kh_key(bamNFOp, bami);
pbam = &kh_value(bamNFOp, bami);
fprintf(stderr, "%u [%s]=%s\t%u %u\n",bami,BamID,pbam->fileName,pbam->insertSize,pbam->SD);
in = sam_open(pbam->fileName, "r");
if (in == NULL) {
fprintf(stderr, "[x]Error opening \"%s\"\n", pbam->fileName);
return EXIT_FAILURE;
}
h = sam_hdr_read(in);
/* out = hts_open("-", "w");
if (out == NULL) {
fprintf(stderr, "[x]Error opening standard output\n");
return EXIT_FAILURE;
}
if (sam_hdr_write(out, h) < 0) {
fprintf(stderr, "[!]Error writing output header.\n");
exit_code = 1;
}
*/
int8_t *ChrIsHum;
if (h == NULL) {
fprintf(stderr, "[x]Couldn't read header for \"%s\"\n", pbam->fileName);
return EXIT_FAILURE;
} else {
ChrIsHum = malloc(h->n_targets * sizeof(int8_t));
for (int32_t i=0; i < h->n_targets; ++i) {
//ChrIsHum[i] = -1;
ki = kh_get(chrNFO, chrNFOp, h->target_name[i]);
if (ki == kh_end(chrNFOp)) {
errx(4,"[x]Cannot find ChrID for [%s] !",h->target_name[i]);
} else {
ChrInfo_t * tmp = &kh_value(chrNFOp, ki);
ChrIsHum[i] = tmp->isHum;
//printf(">>> %d Chr:%s %d\n",i,h->target_name[i],ChrIsHum[i]);
}
}
}
h->ignore_sam_err = 0;
b = bam_init1();
d = bam_init1();
d2 = bam_init1();
if ((idx = sam_index_load(in, pbam->fileName)) == 0) {
fprintf(stderr, "[E::%s] fail to load the BAM index\n", __func__);
return 1;
}
pierCluster = sam_plp_init();
while ((r = sam_read1(in, h, b)) >= 0) {
int8_t flag = false;
const bam1_core_t *c = &b->core;
if (c->flag & BAM_FSECONDARY) continue;
if (c->n_cigar) {
uint32_t *cigar = bam_get_cigar(b);
for (int i = 0; i < c->n_cigar; ++i) {
if (bam_cigar_opchr(cigar[i])=='S') { // soft clipping
if ( bam_cigar_oplen(cigar[i]) >= myConfig.minGrepSlen ) {
flag = true;
}
}
}
}
if (flag && ChrIsHum[c->tid]) { // Now, skip Virus items.
//bam_copy1(bR1, b);
flag = 0; // recycle
//int enoughMapQ = 0;
//kstring_t ks = { 0, 0, NULL };
/*if (sam_format1(h, b, &ks1) < 0) {
fprintf(stderr, "Error writing output.\n");
exit_code = 1;
break;
} else*/ if ((c->mtid == c->tid && ChrIsHum[c->tid]) || (ChrIsHum[c->tid] ^ ChrIsHum[c->mtid])) { // Only grep those mapped on same Human ChrID, or diff species/一方在病毒的情况.
//printf(">[%s]\n",ks_str(&ks1));
flag |= 1;
//tmp_samdat.b = bam_dup1(b);
//kv_push(samdat_t,R1,tmp_samdat);
/*if (checkMapQ(ChrIsHum, b, true)) {
++enoughMapQ;
}*/
}
if (getPairedSam(in, idx, b, d) != 0) {
flag &= ~1;
continue;
} else {
flag |= 2;
/*if (checkMapQ(ChrIsHum, d, false)) {
++enoughMapQ;
}*/
/*if (c->flag & BAM_FSECONDARY) {
if (getPairedSam(in, idx, d, d2) == 0) {
//sam_format1(h, d2, &ks3);
flag |= 4;
if (checkMapQ(ChrIsHum, d2, false)) {
++enoughMapQ;
}
}
}*/
}
/*
对于 BAM_FSECONDARY(256) 的 Read，跳两次 与 读 SA 项，效果一样。
>[sf95_Ref_48245009_48245108_48245208_Vir_-_2000_2044_R_100_90 353 chr2 13996555 0 50S40M chr18 48245109 0ACACAACAATGTTCCGGAGACTCTAAGGCCTCCCGATACAGAGCAGAGGCCACACACACACACACCATGGAATACTATTCAGCCAAAAAA CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC NM:i:0 MD:Z:40 AS:i:40 XS:i:40 RG:Z:Fsimout_mB SA:Z:rgi|59585|emb|X04615.1|,2000,-,40S46M4S,60,0; YC:Z:CT YD:Z:f]
-[sf95_Ref_48245009_48245108_48245208_Vir_-_2000_2044_R_100_90 177 chr18 48245109 9 40S50M gi|59585|emb|X04615.1|2000 0 GTTCCGGAGACTCTAAGGCCTCCCGATACAGAGCAGAGGCCACACACACACACACCATGGAATACTATTCAGCCAAAAAAAGGAATTCAA CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC NM:i:0 MD:Z:50 AS:i:50 XS:i:46 RG:Z:Fsimout_mB SA:Z:rgi|59585|emb|X04615.1|,2000,+,50S40M,9,0; YC:Z:GA YD:Z:f]
+[sf95_Ref_48245009_48245108_48245208_Vir_-_2000_2044_R_100_90 113 gi|59585|emb|X04615.1| 2000 60 40S46M4S chr18 48245109 0 TTTTTTGGCTGAATAGTATTCCATGGTGTGTGTGTGTGTGGCCTCTGCTCTGTATCGGGAGGCCTTAGAGTCTCCGGAACATTGTTGTGT CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC NM:i:0 MD:Z:46 AS:i:46 XS:i:27 RG:Z:Fsimout_mB SA:Z:fchr2,13996555,+,50S40M,0,0; YC:Z:CT YD:Z:r]
*/
/*if (sam_format1(h, d, &ks2) < 0) {
fprintf(stderr, "Error writing output.\n");
exit_code = 1;
break;
}*/
if (((flag & 3) == 3) /*&& enoughMapQ >= myConfig.samples*/) {
/*printf(">%d[%s]\n",checkMapQ(ChrIsHum, b, true),ks_str(&ks1));
printf("-%d[%s]\n",checkMapQ(ChrIsHum, d, false),ks_str(&ks2));
if (flag & 4) {
printf("+%d[%s]\n",checkMapQ(ChrIsHum, d2, false),ks_str(&ks3));
}
printf("<--%d\n",enoughMapQ);*/
if (sam_plp_push(ChrIsHum, pierCluster, b) == 0) {
//printf("--HumRange=%s:%d-%d\n", h->target_name[(pierCluster->HumanRange).tid], (pierCluster->HumanRange).pos, (pierCluster->HumanRange).endpos);
if ((!ChrIsHum[(d->core).tid]) && (flag & 2)) sam_plp_push(ChrIsHum, pierCluster, d);
//if ((!ChrIsHum[(d2->core).tid]) && (flag & 4)) sam_plp_push(ChrIsHum, pierCluster, d2);
} else {
//print
fprintf(fs,"[%s]\nHumRange=%s:%d-%d\n", BamID, h->target_name[(pierCluster->HumanRange).tid], (pierCluster->HumanRange).pos, (pierCluster->HumanRange).endpos);
fprintf(fs,"VirRange=%s:%d-%d\n", h->target_name[(pierCluster->VirusRange).tid], (pierCluster->VirusRange).pos, (pierCluster->VirusRange).endpos);
for (size_t i=0; i<kv_size(pierCluster->Reads);++i) {
bam1_t *bi = kv_A(pierCluster->Reads, i);
if (sam_format1(h, bi, &ks1) < 0) {
fprintf(stderr, "Error writing output.\n");
exit_code = 1;
break;
} else {
fprintf(fs,"%s\n",ks1.s);
}
}
fprintf(fs,"\n");
//printf("HumRange=%s:%d-%d\n", h->target_name[(pierCluster->HumanRange).tid], (pierCluster->HumanRange).pos, (pierCluster->HumanRange).endpos);
//fflush(fs);
sam_plp_dectroy(pierCluster);
pierCluster = sam_plp_init();
}
}
}
/*char *qname = bam_get_qname(b);
if (sam_write1(out, h, b) < 0) {
fprintf(stderr, "[x]Error writing output.\n");
exit_code = 1;
break;
}*/
}
/* r = sam_close(out); // stdout can only be closed once
if (r < 0) {
fprintf(stderr, "Error closing output.\n");
exit_code = 1;
}
*/
hts_idx_destroy(idx);
bam_destroy1(b);
bam_destroy1(d);
bam_destroy1(d2);
bam_hdr_destroy(h);
r = sam_close(in);
free(ChrIsHum);
#ifdef DEBUGa
fflush(NULL);
//pressAnyKey();
#endif
sam_plp_dectroy(pierCluster);
//printf("<[%d]:\n",bami);
}
}
fclose(fs);
getPairedSam(NULL, NULL, NULL, NULL); // sam_close(fp2);
//printf("---[%d]---\n",exit_code);
bam_destroy1(bR1); bam_destroy1(bR2); bam_destroy1(bR3);
ks_release(&ks1);
ks_release(&ks2);
ks_release(&ks3);
return exit_code;
}
static int aux_fields1(void)
{
static const char sam[] = "data:,"
"@SQ\tSN:one\tLN:1000\n"
"@SQ\tSN:two\tLN:500\n"
"r1\t0\tone\t500\t20\t8M\t*\t0\t0\tATGCATGC\tqqqqqqqq\tXA:A:k\tXi:i:37\tXf:f:" xstr(PI) "\tXd:d:" xstr(E) "\tXZ:Z:" HELLO "\tXH:H:" BEEF "\tXB:B:c,-2,0,+2\tB0:B:i,-2147483648,-1,0,1,2147483647\tB1:B:I,0,1,2147483648,4294967295\tB2:B:s,-32768,-1,0,1,32767\tB3:B:S,0,1,32768,65535\tB4:B:c,-128,-1,0,1,127\tB5:B:C,0,1,127,255\tBf:B:f,-3.14159,2.71828\tZZ:i:1000000\tF2:d:2.46801\tY1:i:-2147483648\tY2:i:-2147483647\tY3:i:-1\tY4:i:0\tY5:i:1\tY6:i:2147483647\tY7:i:2147483648\tY8:i:4294967295\n";
// Canonical form of the alignment record above, as output by sam_format1()
static const char r1[] = "r1\t0\tone\t500\t20\t8M\t*\t0\t0\tATGCATGC\tqqqqqqqq\tXi:i:37\tXf:f:3.14159\tXd:d:2.71828\tXZ:Z:" NEW_HELLO "\tXH:H:" BEEF "\tXB:B:c,-2,0,2\tB0:B:i,-2147483648,-1,0,1,2147483647\tB1:B:I,0,1,2147483648,4294967295\tB2:B:s,-32768,-1,0,1,32767\tB3:B:S,0,1,32768,65535\tB4:B:c,-128,-1,0,1,127\tB5:B:C,0,1,127,255\tBf:B:f,-3.14159,2.71828\tZZ:i:1000000\tF2:f:9.8765\tY1:i:-2147483648\tY2:i:-2147483647\tY3:i:-1\tY4:i:0\tY5:i:1\tY6:i:2147483647\tY7:i:2147483648\tY8:i:4294967295\tN0:i:-1234\tN1:i:1234\tN2:i:-2\tN3:i:3\tF1:f:4.5678\tN4:B:S,65535,32768,1,0\tN5:i:4242";
samFile *in = sam_open(sam, "r");
bam_hdr_t *header = sam_hdr_read(in);
bam1_t *aln = bam_init1();
uint8_t *p;
kstring_t ks = { 0, 0, NULL };
int64_t b0vals[5] = { -2147483648LL,-1,0,1,2147483647LL }; // i
int64_t b1vals[4] = { 0,1,2147483648LL,4294967295LL }; // I
int64_t b2vals[5] = { -32768,-1,0,1,32767 }; // s
int64_t b3vals[4] = { 0,1,32768,65535 }; // S
int64_t b4vals[5] = { -128,-1,0,1,127 }; // c
int64_t b5vals[4] = { 0,1,127,255 }; // C
// NB: Floats not doubles below!
// See https://randomascii.wordpress.com/2012/06/26/doubles-are-not-floats-so-dont-compare-them/
float bfvals[2] = { -3.14159f, 2.71828f };
int8_t n4v1[] = { -128, -64, -32, -16, -8, -4, -2, -1,
0, 1, 2, 4, 8, 16, 32, 64, 127 };
uint32_t n4v2[] = { 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 1234, 5678, 1U << 31, 0 };
int16_t n4v3[] = { -32768, -1, 0, 1, 32767 };
float n4v4[] = { 0, 1, 2, 10, 20, 30, 1.5, -2.5 };
uint8_t n4v5[] = { 0, 255 };
int32_t n4v6[] = { -2147483647 - 1, 10, -1, 0, 1, 2147483647 };
uint16_t n4v7[] = { 65535, 32768, 1, 0 };
int32_t ival = -1234;
uint32_t uval = 1234;
float f1 = 4.5678;
float f2 = 9.8765;
size_t nvals, i;
if (sam_read1(in, header, aln) >= 0) {
if ((p = check_bam_aux_get(aln, "XA", 'A')) && bam_aux2A(p) != 'k')
fail("XA field is '%c', expected 'k'", bam_aux2A(p));
bam_aux_del(aln,p);
if (bam_aux_get(aln,"XA"))
fail("XA field was not deleted");
if ((p = check_bam_aux_get(aln, "Xi", 'C')) && bam_aux2i(p) != 37)
fail("Xi field is %"PRId64", expected 37", bam_aux2i(p));
if ((p = check_bam_aux_get(aln, "Xf", 'f')) && fabs(bam_aux2f(p) - PI) > 1E-6)
fail("Xf field is %.12f, expected pi", bam_aux2f(p));
if ((p = check_bam_aux_get(aln, "Xd", 'd')) && fabs(bam_aux2f(p) - E) > 1E-6)
fail("Xf field is %.12f, expected e", bam_aux2f(p));
if ((p = check_bam_aux_get(aln, "XZ", 'Z')) && strcmp(bam_aux2Z(p), HELLO) != 0)
fail("XZ field is \"%s\", expected \"%s\"", bam_aux2Z(p), HELLO);
bam_aux_update_str(aln,"XZ",strlen(NEW_HELLO)+1,NEW_HELLO);
if ((p = check_bam_aux_get(aln, "XZ", 'Z')) && strcmp(bam_aux2Z(p), NEW_HELLO) != 0)
fail("XZ field is \"%s\", expected \"%s\"", bam_aux2Z(p), NEW_HELLO);
if ((p = check_bam_aux_get(aln, "XH", 'H')) && strcmp(bam_aux2Z(p), BEEF) != 0)
fail("XH field is \"%s\", expected \"%s\"", bam_aux2Z(p), BEEF);
if ((p = check_bam_aux_get(aln, "XB", 'B'))
&& ! (memcmp(p, "Bc", 2) == 0
&& memcmp(p + 2, "\x03\x00\x00\x00\xfe\x00\x02", 7) == 0))
fail("XB field is %c,..., expected c,-2,0,+2", p[1]);
check_int_B_array(aln, "B0", NELE(b0vals), b0vals);
check_int_B_array(aln, "B1", NELE(b1vals), b1vals);
check_int_B_array(aln, "B2", NELE(b2vals), b2vals);
check_int_B_array(aln, "B3", NELE(b3vals), b3vals);
check_int_B_array(aln, "B4", NELE(b4vals), b4vals);
check_int_B_array(aln, "B5", NELE(b5vals), b5vals);
nvals = NELE(bfvals);
if ((p = check_bam_aux_get(aln, "Bf", 'B')) != NULL) {
if (bam_auxB_len(p) != nvals)
fail("Wrong length reported for Bf field, got %d, expected %zd\n",
bam_auxB_len(p), nvals);
for (i = 0; i < nvals; i++) {
if (bam_auxB2f(p, i) != bfvals[i]) {
fail("Wrong value from bam_auxB2f for Bf field index %zd, "
"got %f expected %f\n",
i, bam_auxB2f(p, i), bfvals[i]);
}
}
}
if ((p = check_bam_aux_get(aln, "ZZ", 'I')) && bam_aux2i(p) != 1000000)
fail("ZZ field is %"PRId64", expected 1000000", bam_aux2i(p));
if ((p = bam_aux_get(aln, "Y1")) && bam_aux2i(p) != -2147483647-1)
fail("Y1 field is %"PRId64", expected -2^31", bam_aux2i(p));
if ((p = bam_aux_get(aln, "Y2")) && bam_aux2i(p) != -2147483647)
fail("Y2 field is %"PRId64", expected -2^31+1", bam_aux2i(p));
if ((p = bam_aux_get(aln, "Y3")) && bam_aux2i(p) != -1)
fail("Y3 field is %"PRId64", expected -1", bam_aux2i(p));
if ((p = bam_aux_get(aln, "Y4")) && bam_aux2i(p) != 0)
fail("Y4 field is %"PRId64", expected 0", bam_aux2i(p));
if ((p = bam_aux_get(aln, "Y5")) && bam_aux2i(p) != 1)
fail("Y5 field is %"PRId64", expected 1", bam_aux2i(p));
if ((p = bam_aux_get(aln, "Y6")) && bam_aux2i(p) != 2147483647)
fail("Y6 field is %"PRId64", expected 2^31-1", bam_aux2i(p));
if ((p = bam_aux_get(aln, "Y7")) && bam_aux2i(p) != 2147483648LL)
fail("Y7 field is %"PRId64", expected 2^31", bam_aux2i(p));
if ((p = bam_aux_get(aln, "Y8")) && bam_aux2i(p) != 4294967295LL)
fail("Y8 field is %"PRId64", expected 2^32-1", bam_aux2i(p));
// Try appending some new tags
if (bam_aux_append(aln, "N0", 'i', sizeof(ival), (uint8_t *) &ival) != 0)
fail("Failed to append N0:i tag");
if ((p = bam_aux_get(aln, "N0")) && bam_aux2i(p) != ival)
fail("N0 field is %"PRId64", expected %d", bam_aux2i(p), ival);
if (bam_aux_append(aln, "N1", 'I', sizeof(uval), (uint8_t *) &uval) != 0)
fail("failed to append N1:I tag");
if ((p = bam_aux_get(aln, "N1")) && bam_aux2i(p) != uval)
fail("N1 field is %"PRId64", expected %u", bam_aux2i(p), uval);
// Append tags with bam_aux_update_int()
if (bam_aux_update_int(aln, "N2", -2) < 0)
fail("failed to append N2:c tag");
if (bam_aux_update_int(aln, "N3", 3) < 0)
fail("failed to append N3:C tag");
p = bam_aux_get(aln, "N2");
if (!p)
fail("failed to retrieve N2 tag");
else if (*p != 'c' || bam_aux2i(p) != -2)
fail("N2 field is %c:%"PRId64", expected c:-2", *p, bam_aux2i(p));
p = bam_aux_get(aln, "N3");
if (!p)
fail("failed to retrieve N3 tag");
else if (*p != 'C' || bam_aux2i(p) != 3)
fail("N3 field is %c:%"PRId64", expected C:3", *p, bam_aux2i(p));
// Try changing values with bam_aux_update_int()
i = test_update_int(aln, "N2", 2, 'C', "N3", 3, 'C');
if (i == 0) test_update_int(aln, "N2", 1234, 'S', "N3", 3, 'C');
if (i == 0) test_update_int(aln, "N2", -1, 's', "N3", 3, 'C');
if (i == 0) test_update_int(aln, "N2", 4294967295U, 'I', "N3", 3, 'C');
if (i == 0) test_update_int(aln, "N2", -2, 'i', "N3", 3, 'C');
// Append a value with bam_aux_update_float()
if (bam_aux_update_float(aln, "F1", f1) < 0)
fail("append F1:f tag");
p = bam_aux_get(aln, "F1");
if (!p)
fail("retrieve F1 tag");
else if (*p != 'f' || bam_aux2f(p) != f1)
fail("F1 field is %c:%e, expected f:%e", *p, bam_aux2f(p), f1);
// Change a double tag to a float
if (bam_aux_update_float(aln, "F2", f2) < 0)
fail("update F2 tag");
p = bam_aux_get(aln, "F2");
if (!p)
fail("retrieve F2 tag");
else if (*p != 'f' || bam_aux2f(p) != f2)
fail("F2 field is %c:%e, expected f:%e", *p, bam_aux2f(p), f2);
// Check the next one is intact too
p = bam_aux_get(aln, "Y1");
if (!p)
fail("retrieve Y1 tag");
else if (*p != 'i' && bam_aux2i(p) != -2147483647-1)
fail("Y1 field is %"PRId64", expected -2^31", bam_aux2i(p));
// bam_aux_update_array tests
// append a new array
i = test_update_array(aln, "N4", 'c', NELE(n4v1), n4v1, "\0\0", 0, 0);
// Add a sentinal to check resizes work
if (i == 0) i = test_update_int(aln, "N5", 4242, 'S', "\0\0", 0, 0);
// alter the array tag a few times
if (i == 0)
i = test_update_array(aln, "N4", 'I', NELE(n4v2), n4v2,
"N5", 4242, 'S');
if (i == 0)
i = test_update_array(aln, "N4", 's', NELE(n4v3), n4v3,
"N5", 4242, 'S');
if (i == 0)
i = test_update_array(aln, "N4", 'f', NELE(n4v4), n4v4,
"N5", 4242, 'S');
if (i == 0)
i = test_update_array(aln, "N4", 'c', NELE(n4v5), n4v5,
"N5", 4242, 'S');
if (i == 0)
i = test_update_array(aln, "N4", 'i', NELE(n4v6), n4v6,
"N5", 4242, 'S');
if (i == 0)
i = test_update_array(aln, "N4", 'S', NELE(n4v7), n4v7,
"N5", 4242, 'S');
if (sam_format1(header, aln, &ks) < 0)
fail("can't format record");
if (strcmp(ks.s, r1) != 0)
fail("record formatted incorrectly: \"%s\"", ks.s);
free(ks.s);
}
else fail("can't read record");
bam_destroy1(aln);
bam_hdr_destroy(header);
sam_close(in);
return 1;
}
