static rc_t rr_store_make ( rr_store ** rr )
{
rc_t rc;
if ( rr == NULL )
rc = RC ( rcXF, rcFunction, rcConstructing, rcSelf, rcNull );
else
{
KVector * v;
*rr = NULL;
rc = KVectorMake ( &v );
if ( rc == 0 )
{
rr_store * obj = malloc ( sizeof * obj );
if ( obj == NULL )
{
KVectorRelease ( v );
rc = RC ( rcXF, rcFunction, rcConstructing, rcMemory, rcExhausted );
}
else
{
obj -> v = v;
*rr = obj;
}
}
}
return rc;
}
static rc_t TableWriterSeq_CollectStatistics(TableWriterSeq *self, const TableWriterData* primary_alignment_id)
{
rc_t rc;
int64_t mate[2] = {0, 0};
uint64_t distance = 0;
uint64_t count = 0;
memcpy(mate, primary_alignment_id->buffer, sizeof(mate[0]) * primary_alignment_id->elements);
if (mate[0] && mate[1]) {
distance = (mate[0] < mate[1]) ? (mate[1] - mate[0]) : (mate[0] - mate[1]);
}
else
return 0;
if (self->stats == NULL) {
rc = KVectorMake(&self->stats); if (rc) return rc;
}
rc = KVectorGetU64(self->stats, distance, &count);
if (GetRCObject(rc) == rcItem && GetRCState(rc) == rcNotFound) {
rc = KVectorSetU64(self->stats, distance, 1);
if (rc == 0) ++self->statsCount;
}
else if (rc == 0) {
++count;
rc = KVectorSetU64(self->stats, distance, count);
}
return rc;
}
struct rna_splice_dict * make_rna_splice_dict( void )
{
struct rna_splice_dict * res = NULL;
KVector * v;
rc_t rc = KVectorMake ( &v );
if ( rc == 0 )
{
res = calloc( 1, sizeof * res );
if ( res != NULL )
{
res->v = v;
}
else
{
KVectorRelease ( v );
}
}
return res;
}
static rc_t save_store( struct sorter * sorter )
{
rc_t rc = 0;
if ( sorter->bytes_in_store > 0 )
{
char buffer[ 4096 ];
struct lookup_writer * writer;
if ( sorter->params.mem_limit > 0 )
{
rc = make_subfilename( &sorter->params, sorter->sub_file_id, buffer, sizeof buffer );
if ( rc == 0 )
sorter->sub_file_id++;
}
else
rc = make_dst_filename( &sorter->params, buffer, sizeof buffer );
if ( rc == 0 )
rc = make_lookup_writer( sorter->params.dir, NULL, &writer, sorter->params.buf_size, "%s", buffer );
if ( rc == 0 )
{
rc = KVectorVisitPtr( sorter->store, false, on_store_entry, writer );
release_lookup_writer( writer );
}
if ( rc == 0 )
{
sorter->bytes_in_store = 0;
rc = KVectorRelease( sorter->store );
if ( rc != 0 )
ErrMsg( "KVectorRelease() -> %R", rc );
else
{
sorter->store = NULL;
rc = KVectorMake( &sorter->store );
if ( rc != 0 )
ErrMsg( "KVectorMake() -> %R", rc );
}
}
}
return rc;
}
static spotgrp * make_spotgrp( const char *src, const size_t len )
{
spotgrp * sg = calloc( 1, sizeof sg[ 0 ] );
if ( sg != NULL )
{
String s;
StringInit( &s, src, len, len );
if ( StringCopy ( &sg->name, &s ) != 0 )
{
free( sg );
sg = NULL;
}
#ifdef USE_JUDY
else
{
KVectorMake ( &sg->v );
}
#endif
}
return sg;
}
static rc_t init_sorter( struct sorter * sorter, const sorter_params * params )
{
rc_t rc = KVectorMake( &sorter->store );
if ( rc != 0 )
ErrMsg( "KVectorMake() -> %R", rc );
else
{
rc = make_SBuffer( &sorter->buf, 4096 );
if ( rc == 0 )
{
sorter->params.dir = params->dir;
sorter->params.output_filename = params->output_filename;
sorter->params.index_filename = NULL;
sorter->params.temp_path = params->temp_path;
sorter->params.src = params->src;
sorter->params.buf_size = params->buf_size;
sorter->params.mem_limit = params->mem_limit;
sorter->params.prefix = params->prefix;
sorter->bytes_in_store = 0;
sorter->sub_file_id = 0;
}
}
return rc;
}
