static rc_t SRADumper_DumpRun( const SRATable* table,
spotid_t minSpotId, spotid_t maxSpotId, const SRASplitterFactory* factories )
{
rc_t rc = 0, rcr = 0;
spotid_t spot = 0;
make_readmask( readmask );
const SRASplitter* root_splitter = NULL;
rc = SRASplitterFactory_NewObj( factories, &root_splitter );
for( spot = minSpotId; rc == 0 && spot <= maxSpotId; spot++ )
{
reset_readmask( readmask );
rc = SRASplitter_AddSpot( root_splitter, spot, readmask );
rc = rc ? rc : Quitting();
}
rcr = SRASplitter_Release( root_splitter );
return rc ? rc : rcr;
}
/* skip all reads with len < minreadlen */
static
rc_t AbsolidReadLenFilter_GetKey(const SRASplitter* cself, const char** key, spotid_t spot, readmask_t* readmask)
{
rc_t rc = 0;
AbsolidReadLenFilter* self = (AbsolidReadLenFilter*)cself;
if( self == NULL || key == NULL ) {
rc = RC(rcExe, rcNode, rcExecuting, rcParam, rcInvalid);
} else {
*key = "";
if( rc == 0 && (rc = AbsolidReaderSeekSpot(self->reader, spot)) == 0 ) {
uint32_t num_reads = 0;
if( (rc = AbsolidReader_SpotInfo(self->reader, NULL, NULL, NULL, &num_reads)) == 0 ) {
uint32_t readId;
make_readmask(new_mask);
INSDC_coord_len read_len = 0;
clear_readmask(new_mask);
for(readId = 0; rc == 0 && readId < num_reads; readId++) {
if( !isset_readmask(readmask, readId) ) {
continue;
}
rc = AbsolidReader_SpotReadInfo(self->reader, readId + 1, NULL, NULL, NULL, NULL, &read_len);
if( rc == 0 && read_len > 0 ) {
set_readmask(new_mask, readId);
}
}
copy_readmask(new_mask, readmask);
}
} else if( GetRCObject(rc) == rcRow && GetRCState(rc) == rcNotFound ) {
SRA_DUMP_DBG (3, ("%s skipped %u row\n", __func__, spot));
*key = NULL;
rc = 0;
}
}
return rc;
}
/* leave only up to 2 first bio reads */
static
rc_t Absolid2BioFilter_GetKey(const SRASplitter* cself, const char** key, spotid_t spot, readmask_t* readmask)
{
rc_t rc = 0;
Absolid2BioFilter* self = (Absolid2BioFilter*)cself;
if( self == NULL || key == NULL ) {
rc = RC(rcExe, rcNode, rcExecuting, rcParam, rcInvalid);
} else {
if( (rc = AbsolidReaderSeekSpot(self->reader, spot)) == 0 ) {
uint32_t num_reads = 0;
if( (rc = AbsolidReader_SpotInfo(self->reader, NULL, NULL, NULL, &num_reads)) == 0 ) {
uint32_t q, readId;
make_readmask(new_mask);
SRAReadTypes read_type = SRA_READ_TYPE_TECHNICAL;
clear_readmask(new_mask);
for(q = 0, readId = 0; rc == 0 && readId < num_reads && q < 2; readId++) {
if( (rc = AbsolidReader_SpotReadInfo(self->reader, readId + 1, &read_type, NULL, NULL, NULL, NULL)) == 0 ) {
if( read_type & SRA_READ_TYPE_BIOLOGICAL ) {
set_readmask(new_mask, readId);
q++;
}
}
}
*key = "";
copy_readmask(new_mask, readmask);
}
} else if( GetRCObject(rc) == rcRow && GetRCState(rc) == rcNotFound ) {
SRA_DUMP_DBG (3, ("%s skipped %u row\n", __func__, spot));
*key = NULL;
rc = 0;
}
}
return rc;
}
