static
rc_t AbsolidLabelerFilter_GetKeySet(const SRASplitter* cself, const SRASplitter_Keys** key, uint32_t* keys, spotid_t spot, const readmask_t* readmask)
{
rc_t rc = 0;
AbsolidLabelerFilter* self = (AbsolidLabelerFilter*)cself;
if( self == NULL || key == NULL ) {
rc = RC(rcExe, rcNode, rcExecuting, rcParam, rcInvalid);
} else {
*keys = 0;
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, q;
const char* read_label;
INSDC_coord_len read_label_sz = 0;
INSDC_coord_len read_len = 0;
*key = self->keys;
*keys = sizeof(self->keys) / sizeof(self->keys[0]);
for(q = 0; q < *keys; q++) {
clear_readmask(self->keys[q].readmask);
}
for(q = 0, readId = 0; rc == 0 && readId < num_reads; readId++) {
if( !isset_readmask(readmask, readId) ) {
continue;
}
rc = AbsolidReader_SpotReadInfo(self->reader, readId + 1, NULL, &read_label, &read_label_sz, NULL, &read_len);
if( read_len == 0 ) {
continue;
}
if( self->is_platform_cs_native ) {
uint32_t i;
for(i = 0; i < *keys; i++) {
if( read_label_sz == self->key_sz[i] && strncmp(read_label, self->keys[i].key, read_label_sz) == 0 ) {
set_readmask(self->keys[i].readmask, readId);
break;
}
}
if( i >= *keys ) {
rc = RC(rcExe, rcNode, rcExecuting, rcTag, rcUnexpected);
}
} else {
/* since prev filter leaves only 2 first bio reads labels F3 and R3 wil be used */
set_readmask(self->keys[q].readmask, readId);
}
q++;
}
}
} else if( GetRCObject(rc) == rcRow && GetRCState(rc) == rcNotFound ) {
SRA_DUMP_DBG (3, ("%s skipped %u row\n", __func__, spot));
rc = 0;
}
}
return rc;
}
/* 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;
}
static rc_t ReadFilterSplitter_GetKeySet( const SRASplitter* cself,
const SRASplitter_Keys** key, uint32_t* keys, spotid_t spot, const readmask_t* readmask )
{
rc_t rc = 0;
ReadFilterSplitter* self = ( ReadFilterSplitter* )cself;
if ( self == NULL || key == NULL )
{
rc = RC( rcSRA, rcNode, rcExecuting, rcParam, rcNull );
}
else
{
const INSDC_SRA_read_filter* rdf;
bitsz_t o = 0, sz = 0;
*keys = 0;
if ( self->col_rdf != NULL )
{
rc = SRAColumnRead( self->col_rdf, spot, (const void **)&rdf, &o, &sz );
if ( rc == 0 )
{
int32_t j, i = sz / sizeof( INSDC_SRA_read_filter ) / 8;
*key = self->keys;
*keys = sizeof( self->keys ) / sizeof( self->keys[ 0 ] );
for ( j = 0; j < *keys; j++ )
{
clear_readmask( self->keys[ j ].readmask );
}
while ( i > 0 )
{
i--;
if ( self->read_filter != 0xFF && self->read_filter != rdf[i] )
{
/* skip by filter value != to command line */
}
else if ( rdf[ i ] == SRA_READ_FILTER_PASS )
{
set_readmask( self->keys[ EReadFilterSplitter_pass ].readmask, i );
}
else if ( rdf[ i ] == SRA_READ_FILTER_REJECT )
{
set_readmask( self->keys[ EReadFilterSplitter_reject ].readmask, i );
}
else if( rdf[ i ] == SRA_READ_FILTER_CRITERIA )
{
set_readmask( self->keys[ EReadFilterSplitter_criteria ].readmask, i );
}
else if( rdf[ i ] == SRA_READ_FILTER_REDACTED )
{
set_readmask( self->keys[ EReadFilterSplitter_redacted ].readmask, i );
}
else
{
set_readmask( self->keys[ EReadFilterSplitter_unknown ].readmask, i );
PLOGMSG( klogWarn, ( klogWarn,
"unknown READ_FILTER value $(value) at spot id $(row)",
PLOG_2( PLOG_U8( value ), PLOG_I64( row ) ), rdf[ i ], spot ) );
}
}
}
}
}
return rc;
}
