static
rc_t SFFLoaderFmtWriteDataFile(SFFLoaderFmt* self, const SRALoaderFile* file)
{
rc_t rc = 0;
while( rc == 0 ) {
if( self->curr_read_number == 0 ) {
if( (rc = SFFLoaderFmtReadCommonHeader(self, file)) == 0 ) {
DEBUG_MSG (5, ("%s: Common header ok: %u reads\n", self->file_name, self->header.number_of_reads));
DEBUG_MSG (8, ("%s: flow_chars: [%hu] %s\n", self->file_name, self->header.num_flows_per_read, self->flow_chars.data));
DEBUG_MSG (8, ("%s: key_seq: [%hu] %s\n", self->file_name, self->header.key_length, self->key_seq.data));
} else if( GetRCObject(rc) == (enum RCObject)rcData && GetRCState(rc) == rcIgnored ) {
rc = 0;
break;
}
}
if( rc == 0 && self->header.number_of_reads != 0 &&
(rc = SFFLoaderFmtSkipIndex(self, file)) == 0 &&
(rc = SFFLoaderFmtReadDataHeader(self, file)) == 0 &&
(rc = SFFLoaderFmtReadData(self, file)) == 0 ) {
if( self->w454 ) {
rc = SRAWriter454_WriteRead(self->w454, file, &self->name, &self->read, &self->quality,
self->skip_signal ? NULL : &self->signal,
self->skip_signal ? NULL : &self->position,
self->read_header.clip_quality_left, self->read_header.clip_quality_right,
self->read_header.clip_adapter_left, self->read_header.clip_adapter_right);
} else {
rc = SRAWriterIonTorrent_WriteRead(self->wIonTorrent, file, &self->name, &self->read, &self->quality,
self->skip_signal ? NULL : &self->signal,
self->skip_signal ? NULL : &self->position,
self->read_header.clip_quality_left, self->read_header.clip_quality_right,
self->read_header.clip_adapter_left, self->read_header.clip_adapter_right);
}
if( rc == 0 ) {
++self->curr_read_number;
}
}
if( rc != 0 && (GetRCObject(rc) != rcTransfer && GetRCState(rc) != rcDone) ) {
SRALoaderFile_LOG(file, klogErr, rc, "on or about read #$(i)", PLOG_U32(i), self->curr_read_number + 1);
} else if( self->curr_read_number == self->header.number_of_reads ) {
DEBUG_MSG(5, ("%s: done loading declared %u reads\n", self->file_name, self->curr_read_number));
self->curr_read_number = 0;
/* will skip indexes if they are at eof */
if( (rc = SFFLoaderFmtSkipIndex(self, file)) == 0 ) {
/* This should be the end of file and/or beginning of next */
if( (rc = SFFLoaderFmt_ReadBlock(self, file, 0, "EOF", false)) == 0 ) {
if( self->file_buf == NULL ) {
DEBUG_MSG(5, ("%s: EOF detected\n", self->file_name));
self->index_correction = 0;
break;
}
}
}
}
}
return rc;
}
static
rc_t FastqLoaderFmt_WriteData(FastqLoaderFmt* self, uint32_t argc, const SRALoaderFile* const argv[], int64_t* spots_bad_count)
{
rc_t rc = 0;
uint32_t i, g = 0;
FastqFileInfo* files = NULL;
bool done;
static IlluminaSpot spot;
if( (files = calloc(argc, sizeof(*files))) == NULL ) {
rc = RC(rcSRA, rcFormatter, rcReading, rcMemory, rcInsufficient);
}
for(i = 0; rc == 0 && i < argc; i++) {
ExperimentQualityType qType;
FastqFileInfo* file = &files[i];
file->file = argv[i];
FileReadData_init(file->spot, false);
FileReadData_init(&file->spot[1], false);
if( (rc = SRALoaderFile_QualityScoringSystem(file->file, &qType)) == 0 &&
(rc = SRALoaderFile_QualityEncoding(file->file, &file->qualEnc)) == 0 &&
(rc = SRALoaderFile_AsciiOffset(file->file, &file->qualOffset)) == 0 ) {
file->qualType = ILLUMINAWRITER_COLMASK_NOTSET;
if( qType == eExperimentQualityType_Undefined ) {
qType = self->processing->quality_type;
file->qualOffset = self->processing->quality_offset;
}
switch(qType) {
case eExperimentQualityType_LogOdds:
case eExperimentQualityType_Other:
if( self->w454 != NULL || self->wIonTorrent != NULL ) {
rc = RC(rcSRA, rcFormatter, rcConstructing, rcParam, rcInvalid);
LOGERR(klogInt, rc, "quality type other than Phred is not supported for this PLATFORM");
}
file->qualMin = -40;
file->qualMax = 41;
file->qualType = ILLUMINAWRITER_COLMASK_QUALITY_LOGODDS1;
break;
default:
SRALoaderFile_LOG(file->file, klogWarn, rc,
"quality_scoring_system attribute not set for this file, using Phred as default", NULL);
case eExperimentQualityType_Phred:
file->qualType = ILLUMINAWRITER_COLMASK_QUALITY_PHRED;
file->qualMin = 0;
file->qualMax = (self->wIllumina) ? 61: 127;
break;
}
}
}
do {
done = true;
for(i = 0; rc == 0 && i < argc; i++) {
FastqFileInfo* file = &files[i];
if( (rc = read_next_spot(self, file)) != 0 || !file->spot->ready ) {
continue;
}
done = false;
#if _DEBUGGING
{{
FileReadData* ss = file->spot;
do {
DEBUG_MSG(3, ("file-%u: name:'%s', bc:%s, rd:%i, flt:%hu, seq '%.*s', qual %u bytes\n",
i + 1, ss->name.data, ss->barcode.data, ss->read.read_id, ss->read.filter,
ss->read.seq.len, ss->read.seq.data, ss->read.qual.len));
if( ss == &file->spot[1]){ break; }
ss = file->spot[1].ready ? &file->spot[1] : NULL;
} while( ss != NULL );
}}
#endif
}
if( rc != 0 || done ) {
break;
}
/* collect spot reads, matching by spot name
* spot data may be split across multiple files
*/
IlluminaSpot_Init(&spot);
for(i = 0; rc == 0 && i < argc; i++) {
FileReadData* fspot = files[i].spot[0].ready ? &files[i].spot[0] : NULL;
while(rc == 0 && fspot != NULL ) {
rc = IlluminaSpot_Add(&spot, &fspot->name, &fspot->barcode, &fspot->read);
if( rc == 0 ) {
g = i;
fspot->ready = false;
} else if( GetRCState(rc) == rcIgnored ) {
rc = 0;
} else {
SRALoaderFile_LOG(files[i].file, klogErr, rc, "$(msg)", "msg=adding data to spot");
}
if( fspot == &files[i].spot[1]) { break; }
fspot = files[i].spot[1].ready ? &files[i].spot[1] : NULL;
}
}
if( rc == 0 ) {
if( self->wIllumina != NULL ) {
if( (rc = SRAWriterIllumina_Write(self->wIllumina, argv[0], &spot)) != 0 &&
GetRCTarget(rc) == rcFormatter && GetRCContext(rc) == rcValidating ) {
SRALoaderFile_LOG(files[g].file, klogWarn, rc, "$(msg) $(spot_name)", "msg=bad spot,spot_name=%.*s",
spot.name->len, spot.name->data);
self->spots_bad_count++;
if( self->spots_bad_allowed < 0 ||
self->spots_bad_count <= self->spots_bad_allowed ) {
rc = 0;
}
}
} else if( spot.nreads != 1 ) {
rc = RC(rcSRA, rcFormatter, rcReading, rcData, rcUnsupported);
SRALoaderFile_LOG(files[g].file, klogErr, rc, "$(msg)", "msg=multiple reads for this platform");
} else if( self->wIonTorrent != NULL ) {
rc = SRAWriterIonTorrent_WriteRead(self->wIonTorrent, argv[0], spot.name,
spot.reads[0].seq, spot.reads[0].qual, NULL, NULL, 0, 0, 0, 0);
} else {
rc = SRAWriter454_WriteRead(self->w454, argv[0], spot.name,
spot.reads[0].seq, spot.reads[0].qual, NULL, NULL, 0, 0, 0, 0);
}
}
} while( rc == 0 );
free(files);
*spots_bad_count = self->spots_bad_count;
return rc;
}