static
rc_t CC CGEvidenceIntervals20_Read(const CGEvidenceIntervals15* cself, TEvidenceIntervalsData* data)
{
rc_t rc = 0;
CG_LINE_START(cself->file, b, len, p);
if( b == NULL || len == 0) {
rc = RC(rcRuntime, rcFile, rcReading, rcData, rcDone);
break;
}
/*DEBUG_MSG(10, ("evidenceIntervals: '%.*s'\n", len, b));*/
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2buf(b, p - b, data->interval_id, sizeof(data->interval_id));
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2buf(b, p - b, data->chr, sizeof(data->chr));
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2i32(b, p - b, &data->offset);
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2u32(b, p - b, &data->length);
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2u16(b, p - b, &data->ploidy);
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2buf(b, p - b, data->allele_indexes, sizeof(data->allele_indexes));
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2i32(b, p - b, &data->scoreVAF);
data->score = data->scoreVAF; /***TODO: do we need re-calculation? ***/
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2i32(b, p - b, &data->scoreEAF);
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2buf(b, p - b, data->allele[0], sizeof(data->allele[0]));
data->allele_length[0] = p - b;
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2buf(b, p - b, data->allele[1], sizeof(data->allele[1]));
data->allele_length[1] = p - b;
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2buf(b, p - b, data->allele[2], sizeof(data->allele[2]));
data->allele_length[2] = p - b;
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2buf(b, p - b, data->allele[3], sizeof(data->allele[3]));
data->allele_length[3] = p - b;
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2buf(b, p - b, data->allele_alignment[1], sizeof(data->allele_alignment[1]));
data->allele_alignment_length[1] = p - b;
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2buf(b, p - b, data->allele_alignment[2], sizeof(data->allele_alignment[2]));
data->allele_alignment_length[2] = p - b;
CG_LINE_LAST_FIELD(b, len, p);
rc = str2buf(b, p - b, data->allele_alignment[3], sizeof(data->allele_alignment[3]));
data->allele_alignment_length[3] = p - b;
((CGEvidenceIntervals15*)cself)->records++;
DEBUG_MSG(10, (
"evidenceIntervals: '%s'\t'%s'\t%i\t%u\t%u\t%s\t%u\t%u\t'%s'\t'%s'\t'%s'\t'%s'\t'%s'\t'%s'\t'%s'\n",
data->interval_id, data->chr, data->offset, data->length, data->ploidy,
data->allele_indexes, data->scoreVAF, data->scoreEAF,
data->allele[0], data->allele[1], data->allele[2], data->allele[3],
data->allele_alignment[1], data->allele_alignment[2], data->allele_alignment[3]));
CG_LINE_END();
return rc;
}
static
rc_t CC CGReads15_Header(const CGReads15* cself, const char* buf, const size_t len)
{
rc_t rc = 0;
size_t slen;
CGReads15* self = (CGReads15*)cself;
if( strncmp("ASSEMBLY_ID\t", buf, slen = 12) == 0 ) {
rc = str2buf(&buf[slen], len - slen, self->assembly_id, sizeof(self->assembly_id));
} else if( strncmp("BATCH_FILE_NUMBER\t", buf, slen = 18) == 0 ) {
rc = str2u32(&buf[slen], len - slen, &self->batch_file_number);
if( self->batch_file_number < 1 ) {
rc = RC(rcRuntime, rcFile, rcConstructing, rcItem, rcOutofrange);
}
} else if( strncmp("BATCH_OFFSET\t", buf, slen = 13) == 0 ) {
rc = str2u64(&buf[slen], len - slen, &self->batch_offset);
} else if( strncmp("FIELD_SIZE\t", buf, slen = 11) == 0 ) {
rc = str2u32(&buf[slen], len - slen, &self->field_size);
} else if( strncmp("GENERATED_AT\t", buf, slen = 13) == 0 ) {
rc = str2buf(&buf[slen], len - slen, self->generated_at, sizeof(self->generated_at));
} else if( strncmp("GENERATED_BY\t", buf, slen = 13) == 0 ) {
rc = str2buf(&buf[slen], len - slen, self->generated_by, sizeof(self->generated_by));
} else if( strncmp("LANE\t", buf, slen = 5) == 0 ) {
rc = str2buf(&buf[slen], len - slen, self->lane, sizeof(self->lane));
} else if( strncmp("LIBRARY\t", buf, slen = 8) == 0 ) {
rc = str2buf(&buf[slen], len - slen, self->library, sizeof(self->library));
} else if( strncmp("SAMPLE\t", buf, slen = 7) == 0 ) {
rc = str2buf(&buf[slen], len - slen, self->sample, sizeof(self->sample));
} else if( strncmp("SLIDE\t", buf, slen = 6) == 0 ) {
rc = str2buf(&buf[slen], len - slen, self->slide, sizeof(self->slide));
} else if( strncmp("SOFTWARE_VERSION\t", buf, slen = 17) == 0 ) {
rc = str2buf(&buf[slen], len - slen, self->software_version, sizeof(self->software_version));
} else {
rc = RC(rcRuntime, rcFile, rcConstructing, rcName, rcUnrecognized);
}
return rc;
}
static rc_t CC CGReads25_Header(const CGReads15* cself,
const char* buf, const size_t len)
{
rc_t rc = 0;
size_t slen = 0;
CGReads15* self = (CGReads15*)cself;
/* from SRA-2617 files */
if (strncmp("APPROVAL\t", buf, slen = 9) == 0) {
}
else if (strncmp("TITLE\t", buf, slen = 6) == 0) {
}
else if (strncmp("ADDRESS\t", buf, slen = 8) == 0) {
}
/* From Table 1: Header Metadata Present in all Data Files */
else if (strncmp("CUSTOMER_SAMPLE_ID\t", buf, slen = 19) == 0) {
}
else if (strncmp("SAMPLE_SOURCE\t", buf, slen = 14) == 0) {
}
else if (strncmp("REPORTED_GENDER\t", buf, slen = 16) == 0) {
}
else if (strncmp("CALLED_GENDER\t", buf, slen = 14) == 0) {
}
else if (strncmp("TUMOR_STATUS\t", buf, slen = 13) == 0) {
}
else if (strncmp("LIBRARY_TYPE\t", buf, slen = 13) == 0) {
}
else if (strncmp("LIBRARY_SOURCE\t", buf, slen = 13) == 0) {
}
else if (strncmp("ASSEMBLY_ID\t", buf, slen = 12) == 0) {
rc = str2buf(&buf[slen], len - slen,
self->assembly_id, sizeof(self->assembly_id));
}
else if (strncmp("BATCH_FILE_NUMBER\t", buf, slen = 18) == 0) {
rc = str2u32(&buf[slen], len - slen, &self->batch_file_number);
if (self->batch_file_number < 1) {
rc = RC(rcRuntime, rcFile, rcConstructing, rcItem, rcOutofrange);
}
}
else if (strncmp("BATCH_OFFSET\t", buf, slen = 13) == 0) {
rc = str2u64(&buf[slen], len - slen, &self->batch_offset);
}
else if (strncmp("FIELD_SIZE\t", buf, slen = 11) == 0) {
rc = str2u32(&buf[slen], len - slen, &self->field_size);
}
else if (strncmp("GENERATED_AT\t", buf, slen = 13) == 0) {
rc = str2buf(&buf[slen], len - slen,
self->generated_at, sizeof(self->generated_at));
}
else if (strncmp("GENERATED_BY\t", buf, slen = 13) == 0) {
rc = str2buf(&buf[slen], len - slen,
self->generated_by, sizeof(self->generated_by));
}
else if (strncmp("LANE\t", buf, slen = 5) == 0) {
rc = str2buf(&buf[slen], len - slen,
self->lane, sizeof(self->lane));
}
else if (strncmp("LIBRARY\t", buf, slen = 8) == 0) {
rc = str2buf(&buf[slen], len - slen,
self->library, sizeof(self->library));
}
else if (strncmp("SAMPLE\t", buf, slen = 7) == 0) {
rc = str2buf(&buf[slen], len - slen,
self->sample, sizeof(self->sample));
}
else if (strncmp("SLIDE\t", buf, slen = 6) == 0) {
rc = str2buf(&buf[slen], len - slen, self->slide, sizeof(self->slide));
}
else if (strncmp("SOFTWARE_VERSION\t", buf, slen = 17) == 0) {
rc = str2buf(&buf[slen], len - slen,
self->software_version, sizeof(self->software_version));
}
else {
rc = RC(rcRuntime, rcFile, rcConstructing, rcName, rcUnrecognized);
}
return rc;
}
int main(int argc, char* argv[])
{
int o, rc;
memset(&im, 0, sizeof(im));
strcpy(im.outputfile, DEFAULT_OUTPUT_FILE);
strcpy(im.version, DEFAULT_VERSION);
memcpy(im.magic, MAGIC_HEADER, MAGIC_LENGTH);
im.flash_baseaddr = DEFAULT_FLASH_BASE;
while ((o = getopt(argc, argv, "f:hm:o:p:v:z")) != -1)
{
switch (o) {
case 'f':
if (optarg)
if (str2u32(optarg, &im.flash_baseaddr)) {
ERROR("Invalid flash start address %s\n", optarg);
return -1;
}
break;
case 'h':
usage(argv[0]);
return -1;
case 'm':
if (optarg) {
if (strlen(optarg) != MAGIC_LENGTH) {
ERROR("Invalid magic %s\n", optarg);
return -1;
}
memcpy(im.magic, optarg, MAGIC_LENGTH);
}
break;
case 'o':
if (optarg)
strncpy(im.outputfile, optarg, sizeof(im.outputfile));
break;
case 'p':
if (optarg) {
if (image_layout_add_partition(optarg))
return -1;
}
break;
case 'v':
if (optarg)
strncpy(im.version, optarg, sizeof(im.version));
break;
case 'z':
zero_part_baseaddr = 1;
break;
}
}
rc = image_layout_verify();
if (rc) {
ERROR("Failed validating firmware layout - error code: %d\n",
rc);
return -4;
}
print_image_info();
rc = build_image();
if (rc) {
ERROR("Failed building image file '%s' - error code: %d\n",
im.outputfile, rc);
return -5;
}
return 0;
}
static int image_layout_add_partition(const char *part_desc)
{
part_data_t *d;
char memaddr[16];
char entryaddr[16];
char offset[16];
char length[16];
int t;
if (im.part_count >= MAX_SECTIONS) {
ERROR("Too many partitions specified\n");
return (-1);
}
d = &im.parts[im.part_count];
t = sscanf(part_desc, "%15[0-9a-zA-Z]:%15[0-9a-fA-Fx]:%15[0-9a-fA-Fx]:%15[0-9a-fA-Fx]:%15[0-9a-fA-Fx]:%256s",
d->partition_name,
offset,
length,
memaddr,
entryaddr,
d->filename);
if (t != 6) {
ERROR("Bad partition parameter %d, '%s'\n", t, part_desc);
return (-1);
}
if (strlen(d->partition_name) == 0) {
ERROR("No partition name specified in '%s'\n", part_desc);
return (-1);
}
if (str2u32(offset, &d->partition_offset)) {
ERROR("Bad offset value '%s'\n", offset);
return (-1);
}
if (str2u32(length, &d->partition_length)) {
ERROR("Bad length value '%s'\n", length);
return (-1);
}
if (d->partition_length == 0) {
int flen;
flen = filelength(d->filename);
if (flen < 0) {
ERROR("Unable to determine size of '%s'\n",
d->filename);
return (-1);
}
d->partition_length = flen;
}
if (str2u32(memaddr, &d->partition_memaddr)) {
ERROR("Bad memaddr vaule '%s'\n", memaddr);
return (-1);
}
if (str2u32(entryaddr, &d->partition_entryaddr)) {
ERROR("Bad entry address value '%s'\n", entryaddr);
return (-1);
}
im.part_count++;
d->partition_index = im.part_count;
return 0;
}
// Reads a LAMMPS input file.
void LAMMPS_Data::read_data(string path) {
fstream fid(path);
if (!fid) {
cout << "Error opening output file " << path << "!\n";
}
int section=0;
while (fid) {
auto line = split(read_line(fid));
if (line.empty()) continue;
else if (line[0]=="Masses") section=1;
else if (line[0]=="Pair") section=2;
else if (line[0]=="Bond") section=3;
else if (line[0]=="Angle") section=4;
else if (line[0]=="Dihedral") section=5;
else if (line[0]=="Atoms") section=6;
else if (line[0]=="Bonds") section=7;
else if (line[0]=="Angles") section=8;
else if (line[0]=="Dihedrals") section=9;
switch (section) {
case 1:
if (line.size()==2) {
//_system.atom_types.push_back(str2u32(line[0]));
//_system.masses.push_back(str2dbl(line[1]));
}
break;
case 6:
Atom newatom;
if (line.size() >= 6) {
newatom.molecule = str2u32(line[1]);
newatom.type = str2u32(line[2]);
_system.atoms.push_back(newatom);
}
break;
case 7:
if (_system.connect.empty()) {
_system.connect.assign(_system.atoms.size(), vector<int>(0));
}
if (line.size()==4) {
Bond newbond;
//newbond.id = str2u32(line[0]);
//newbond.type = str2u32(line[1]);
newbond.atom1 = str2u32(line[2])-1;
newbond.atom2 = str2u32(line[3])-1;
//_system.bonds.push_back(newbond);
_system.connect[newbond.atom1].push_back(newbond.atom2);
_system.connect[newbond.atom2].push_back(newbond.atom1);
}
break;
case 8: break; // No need to keep going.
default: continue;
};
}
// Report total number of bonds.
int num_bonds = 0;
for (auto c=_system.connect.cbegin(); c!=_system.connect.cend(); ++c) {
num_bonds += c->size();
}
cout << "Read " << num_bonds/2 << " bonds from the input file.\n";
}
// Reads a LAMMPS dump output file, in atom format.
void LAMMPS_Data::read_dump(string path) {
fstream fid(path);
if (!fid) cout << "Error opening output file " << path << "!\n";
else cout << "Opened dump " << path << ".\n";
SnapshotDump *step=NULL;
while (fid) {
auto line = trim(read_line(fid));
if (line.empty()) continue;
else if (line=="ITEM: TIMESTEP") {
_dump.push_back(SnapshotDump());
step = &_dump.back();
step->timestep = str2u32(trim(read_line(fid)));
}
else if (line=="ITEM: NUMBER OF ATOMS") {
if (!step) {
cout << "Error: NUMBER OF ATOMS specified before TIMESTEP\n";
exit(1);
}
unsigned n = str2u32(trim(read_line(fid)));
step->scaled_coordinates.assign(n, Coord());
}
else if (line.find("ITEM: BOX BOUNDS")==0) {
if (!step) {
cout << "Error: BOX BOUNDS specified before TIMESTEP\n";
exit(1);
}
auto xb = split(read_line(fid));
auto yb = split(read_line(fid));
auto zb = split(read_line(fid));
step->dx = fabs(str2dbl(xb.at(1))-str2dbl(xb.at(0)));
step->dy = fabs(str2dbl(yb.at(1))-str2dbl(yb.at(0)));
step->dz = fabs(str2dbl(zb.at(1))-str2dbl(zb.at(0)));
}
// The only thing left should be the ATOMS data.
else {
auto pieces = split(line);
if (pieces.size() < 4) continue;
if (pieces[0]=="ITEM:" && pieces[1]=="ATOMS") {
vector<string> var(pieces.begin()+2, pieces.end());
// Search for coordinate and tag columns.
step->xc = step->yc = step->zc = step->zc = -1;
step->xs = step->ys = step->zs = 0;
for (size_t i=0; i<var.size(); ++i) {
if (var[i]=="x") {step->xc=i;}
if (var[i]=="xs") {step->xc=i; step->xs=1; }
if (var[i]=="y") {step->yc=i;}
if (var[i]=="ys") {step->yc=i; step->ys=1; }
if (var[i]=="z") {step->zc=i;}
if (var[i]=="zs") {step->zc=i; step->zs=1; }
if (var[i]=="id") step->tc=i;
}
if (step->xc<0 || step->yc<0 || step->zc<0) {
cout << "Error: coordinate column not found\n";
exit(1);
}
if (step->tc<0) {
cout << "Error: atom tag column not found.\n";
exit(1);
}
continue;
}
if (!step) {
cout << "Error: data encountered before TIMESTEP\n";
exit(1);
}
auto maxc=max(step->tc,max(step->xc,max(step->yc,step->zc)));
auto minc=min(step->tc,min(step->xc,min(step->yc,step->zc)));
if (maxc >= (int)pieces.size()) {
cout << "Not enough columns in dump data.\n";
exit(1);
}
if (minc < 0) {
cout << "Missing data column in dump data.\n";
exit(1);
}
unsigned id = str2u32(pieces[step->tc])-1;
if (step->scaled_coordinates.size() <= id) {
cout << "Error: invalid atom id found " << id << "\n";
exit(1);
}
Coord &r = step->scaled_coordinates[id];
r.x = str2dbl(pieces[step->xc]);
r.y = str2dbl(pieces[step->yc]);
r.z = str2dbl(pieces[step->zc]);
// Store coordinates scaled no matter what the input is.
if (!step->xs) r.x = to_scaled(r.x, step->dx);
if (!step->ys) r.y = to_scaled(r.y, step->dy);
if (!step->zs) r.z = to_scaled(r.z, step->dz);
}
}
}
static
rc_t CC CGEvidenceDnbs_Read(const CGEvidenceDnbs15* cself, const char* interval_id, TEvidenceDnbsData* data, int score_allele_num)
{
rc_t rc = 0;
TEvidenceDnbsData_dnb* m = NULL;
static TEvidenceDnbsData_dnb next_rec;
static char next_interval_id[32] = "";
/* local copy of unused TEvidenceDnbsData_dnb struct elements */
char reference_alignment[CG_EVDNC_ALLELE_CIGAR_LEN];
INSDC_coord_zero mate_offset_in_reference;
char mate_reference_alignment[CG_EVDNC_ALLELE_CIGAR_LEN];
uint16_t score_allele[4] = {0, 0, 0, 0}; /* v1.5 has ScoreAllele[012]; v2.0 - [0123] */
char qual[CG_EVDNC_SPOT_LEN];
strcpy(data->interval_id, interval_id);
data->qty = 0;
/* already read one rec for this interval_id */
if( next_interval_id[0] != '\0' ) {
if( strcmp(next_interval_id, interval_id) != 0 ) {
/* nothing todo since next interval id is different */
return rc;
}
m = &data->dnbs[data->qty++];
memcpy(m, &next_rec, sizeof(next_rec));
DEBUG_MSG(10, ("%3u evidenceDnbs: '%s'\t'%s'\t'%s'\t'%s'\t%u\t%lu\t%hu\t%c\t%c\t%i\t'%.*s'"
"\t%i\tnot_used\t0\tnot_used\t%c\t0\t0\t0\t'%.*s'\t'--'\n",
data->qty, next_interval_id, m->chr, m->slide, m->lane, m->file_num_in_lane,
m->dnb_offset_in_lane_file, m->allele_index, m->side, m->strand, m->offset_in_allele,
m->allele_alignment_length, m->allele_alignment, m->offset_in_reference,
m->mapping_quality, m->read_len, m->read));
}
do {
int i = 0;
char tmp[2];
CG_LINE_START(cself->file, b, len, p);
if( b == NULL || len == 0 ) {
next_interval_id[0] = '\0';
break; /* EOF */
}
if( data->qty >= data->max_qty ) {
TEvidenceDnbsData_dnb* x;
data->max_qty += 100;
x = realloc(data->dnbs, sizeof(*(data->dnbs)) * data->max_qty);
if( x == NULL ) {
rc = RC(rcRuntime, rcFile, rcReading, rcMemory, rcExhausted);
break;
}
data->dnbs = x;
}
m = &data->dnbs[data->qty++];
/*DEBUG_MSG(10, ("%2hu evidenceDnbs: '%.*s'\n", data->qty, len, b));*/
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2buf(b, p - b, next_interval_id, sizeof(next_interval_id));
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2buf(b, p - b, m->chr, sizeof(m->chr));
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2buf(b, p - b, m->slide, sizeof(m->slide));
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2buf(b, p - b, m->lane, sizeof(m->lane));
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2u32(b, p - b, &m->file_num_in_lane);
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2u64(b, p - b, &m->dnb_offset_in_lane_file);
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2u16(b, p - b, &m->allele_index);
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2buf(b, p - b, tmp, sizeof(tmp));
if( tmp[0] != 'L' && tmp[0] != 'R' ) {
rc = RC(rcRuntime, rcFile, rcReading, rcData, rcOutofrange);
}
m->side = tmp[0];
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2buf(b, p - b, tmp, sizeof(tmp));
if( tmp[0] != '+' && tmp[0] != '-' ) {
rc = RC(rcRuntime, rcFile, rcReading, rcData, rcOutofrange);
}
m->strand = tmp[0];
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2i32(b, p - b, &m->offset_in_allele);
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2buf(b, p - b, m->allele_alignment, sizeof(m->allele_alignment));
m->allele_alignment_length = p - b;
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2i32(b, p - b, &m->offset_in_reference);
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2buf(b, p - b, reference_alignment, sizeof(reference_alignment));
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2i32(b, p - b, &mate_offset_in_reference);
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2buf(b, p - b, mate_reference_alignment, sizeof(mate_reference_alignment));
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2buf(b, p - b, tmp, sizeof(tmp));
if( tmp[0] < 33 || tmp[0] > 126 ) {
rc = RC(rcRuntime, rcFile, rcReading, rcData, rcOutofrange);
}
m->mapping_quality = tmp[0];
for (i = 0; i < score_allele_num; ++i) {
CG_LINE_NEXT_FIELD(b, len, p);
rc = str2u16(b, p - b, &score_allele[i]);
if(rc){
score_allele[i] =0;
rc =0;
}
}
CG_LINE_NEXT_FIELD(b, len, p);
m->read_len = p - b;
rc = str2buf(b, m->read_len, m->read, sizeof(m->read));
CG_LINE_LAST_FIELD(b, len, p);
if( m->read_len != p - b ) {
rc = RC(rcRuntime, rcFile, rcReading, rcData, rcInconsistent);
} else {
rc = str2buf(b, p - b, qual, sizeof(qual));
}
((CGEvidenceDnbs15*)cself)->records++;
if( strcmp(next_interval_id, data->interval_id) != 0 ) {
if (score_allele_num == 3) {
DEBUG_MSG(10, ("%3u evidenceDnbs: '%s'\t'%s'\t'%s'\t'%s'\t%u\t%lu\t%hu\t%c\t%c\t%i\t'%.*s'"
"\t%i\t'%s'\t%i\t'%s'\t%c\t%hu\t%hu\t%hu\t'%.*s'\t'%s'\n",
data->qty, next_interval_id, m->chr, m->slide, m->lane, m->file_num_in_lane,
m->dnb_offset_in_lane_file, m->allele_index, m->side, m->strand, m->offset_in_allele,
m->allele_alignment_length, m->allele_alignment, m->offset_in_reference,
reference_alignment, mate_offset_in_reference, mate_reference_alignment,
m->mapping_quality, score_allele[0], score_allele[1], score_allele[2], m->read_len, m->read, qual));
}
else if (score_allele_num == 4) {
DEBUG_MSG(10, ("%3u evidenceDnbs: '%s'\t'%s'\t'%s'\t'%s'\t%u\t%lu\t%hu\t%c\t%c\t%i\t'%.*s'"
"\t%i\t'%s'\t%i\t'%s'\t%c\t%hu\t%hu\t%hu\t%hu\t'%.*s'\t'%s'\n",
data->qty, next_interval_id, m->chr, m->slide, m->lane, m->file_num_in_lane,
m->dnb_offset_in_lane_file, m->allele_index, m->side, m->strand, m->offset_in_allele,
m->allele_alignment_length, m->allele_alignment, m->offset_in_reference,
reference_alignment, mate_offset_in_reference, mate_reference_alignment,
m->mapping_quality, score_allele[0], score_allele[1], score_allele[2], score_allele[3], m->read_len, m->read, qual));
}
else { assert(0); }
}
CG_LINE_END();
if( next_interval_id[0] == '\0' ) {
break;
}
if( strcmp(next_interval_id, data->interval_id) != 0 ) {
/* next record is from next interval, remeber it and stop */
memcpy(&next_rec, m, sizeof(next_rec));
data->qty--;
break;
}
} while( rc == 0 );
return rc;
}
