CVDB::CVDB(const CVDBMgr& mgr, const string& acc_or_path)
: m_Name(acc_or_path)
{
DECLARE_SDK_GUARD();
string path = CVPath::ConvertAccOrSysPathToPOSIX(acc_or_path);
if ( rc_t rc = VDBManagerOpenDBRead(mgr, x_InitPtr(), 0, "%.*s",
int(path.size()), path.data()) ) {
*x_InitPtr() = 0;
if ( (GetRCObject(rc) == RCObject(rcDirectory) ||
GetRCObject(rc) == RCObject(rcPath) ||
GetRCObject(rc) == RCObject(rcFile)) &&
GetRCState(rc) == rcNotFound ) {
// no SRA accession
NCBI_THROW2_FMT(CSraException, eNotFoundDb,
"Cannot open VDB: "<<acc_or_path, rc);
}
else if ( GetRCObject(rc) == rcName &&
GetRCState(rc) == rcNotFound &&
GetRCContext(rc) == rcResolving ) {
// invalid SRA database
NCBI_THROW2_FMT(CSraException, eNotFoundDb,
"Cannot open VDB: "<<acc_or_path, rc);
}
else if ( GetRCObject(rc) == RCObject(rcFile) &&
GetRCState(rc) == rcUnauthorized ) {
// invalid SRA database
NCBI_THROW2_FMT(CSraException, eProtectedDb,
"Cannot open VDB: "<<acc_or_path, rc);
}
else if ( GetRCObject(rc) == RCObject(rcDatabase) &&
GetRCState(rc) == rcIncorrect ) {
// invalid SRA database
NCBI_THROW2_FMT(CSraException, eDataError,
"Cannot open VDB: "<<acc_or_path, rc);
}
else {
// other errors
NCBI_THROW2_FMT(CSraException, eOtherError,
"Cannot open VDB: "<<acc_or_path, 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;
}
size_t KWrtFmt_rc_t ( char * pout, size_t max, const char * fmt, rc_t rc_in )
{
rc_t rc;
const char * str;
const char * mod_str;
const char * targ_str;
const char * ctx_str;
const char * obj_str;
const char * state_str;
size_t needed;
size_t mod_size;
size_t targ_size;
size_t ctx_size;
size_t obj_size;
size_t state_size;
enum RCModule mod;
enum RCTarget targ;
enum RCContext ctx;
int obj;
enum RCState state;
assert (pout);
assert (fmt);
if (*fmt == '#')
rc = RCExplain (rc_in, pout, max, &needed);
else if (rc_in != 0)
{
mod = GetRCModule (rc_in);
targ = GetRCTarget (rc_in);
ctx = GetRCContext (rc_in);
obj = GetRCObject (rc_in);
state = GetRCState (rc_in);
if ((mod < 0) || (mod > rcLastModule_v1_1))
mod = rcLastModule_v1_1;
if ((targ < 0) || (targ > rcLastTarget_v1_1))
targ = rcLastTarget_v1_1;
if ((ctx < 0) || (ctx > rcLastContext_v1_1))
ctx = rcLastContext_v1_1;
if ((obj < 0) || (obj > rcLastObject_v1_1))
obj = rcLastObject_v1_1;
if ((state < 0) || (state > rcLastState_v1_1))
state = rcLastState_v1_1;
mod_str = RCModuleStrings[mod];
str = strchrnul(mod_str, ' ');
mod_size = str - mod_str;
targ_str = RCTargetStrings[targ];
str = strchrnul(targ_str, ' ');
targ_size = str - targ_str;
ctx_str = RCContextStrings[ctx];
str = strchrnul(ctx_str, ' ');
ctx_size = str - ctx_str;
/* object is tricky because it overlaps target */
if (obj == 0)
{
obj_str = RCObjectStrings[obj];
str = strchrnul(obj_str, ' ');
obj_size = str - obj_str;
}
else if (obj < rcLastTarget_v1_1)
{
obj_str = RCTargetStrings[obj];
str = strchrnul(obj_str, ' ');
obj_size = str - obj_str;
}
else
{
obj -= (rcLastTarget_v1_1-1);
obj_str = RCObjectStrings[obj];
str = strchrnul(obj_str, ' ');
obj_size = str - obj_str;
}
state_str = RCStateStrings[state];
str = strchrnul(state_str, ' ');
state_size = str - state_str;
#if _DEBUGGING
rc = string_printf (pout, max, & needed, "RC(%s:%u:%s %*s,%*s,%*s,%*s,%*s)",
GetRCFilename(), GetRCLineno(), GetRCFunction(),
(uint32_t)mod_size, mod_str,
(uint32_t)targ_size, targ_str,
(uint32_t)ctx_size, ctx_str,
(uint32_t)obj_size, obj_str,
(uint32_t)state_size, state_str);
#else
rc = string_printf (pout, max, & needed, "RC(%*s,%*s,%*s,%*s,%*s)",
(uint32_t)mod_size, mod_str,
(uint32_t)targ_size, targ_str,
(uint32_t)ctx_size, ctx_str,
(uint32_t)obj_size, obj_str,
(uint32_t)state_size, state_str);
#endif
}
else
{
state = GetRCState (rc_in);
state_str = RCStateStrings[state];
str = strchrnul(state_str, ' ');
state_size = str - state_str;
rc = string_printf (pout, max, & needed, "RC(%*s)",
(uint32_t)state_size, state_str);
}
return rc != 0 ? 0 : needed;
}