int call_align ( int argc, char ** argv )
{
time_t start_t, stop_t, time_bef, time_aft;
time ( &start_t );
initenv ( argc, argv );
overlaplen = getMinOverlap ( graphfile );
printf ( "K = %d\n", overlaplen );
time ( &time_bef );
ctg_short = overlaplen + 2;
printf ( "contig len cutoff: %d\n", ctg_short );
prlContig2nodes ( graphfile, ctg_short );
time ( &time_aft );
printf ( "time spent on De bruijn graph construction: %ds\n\n",
( int ) ( time_aft - time_bef ) );
//map long read to edge one by one
time ( &time_bef );
prlLongRead2Ctg ( shortrdsfile, graphfile );
time ( &time_aft );
printf ( "time spent on mapping long reads: %ds\n\n", ( int ) ( time_aft - time_bef ) );
//map read to edge one by one
time ( &time_bef );
prlRead2Ctg ( shortrdsfile, graphfile );
time ( &time_aft );
printf ( "time spent on mapping reads: %ds\n\n", ( int ) ( time_aft - time_bef ) );
free_Sets ( KmerSets, thrd_num );
time ( &stop_t );
printf ( "overall time for alignment: %dm\n\n", ( int ) ( stop_t - start_t ) / 60 );
return 0;
}
int call_align ( int argc, char ** argv )
{
time_t start_t, stop_t, time_bef, time_aft;
time ( &start_t );
fprintf ( stderr, "\n********************\n" );
fprintf ( stderr, "Map\n" );
fprintf ( stderr, "********************\n\n" );
initenv ( argc, argv );
overlaplen = getMinOverlap ( graphfile );
#ifdef MER127
if ( smallKmer > 12 && smallKmer < 128 && smallKmer % 2 == 1 )
{
deltaKmer = overlaplen - smallKmer;
overlaplen = smallKmer;
}
#else
if ( smallKmer > 12 && smallKmer < 64 && smallKmer % 2 == 1 )
{
deltaKmer = overlaplen - smallKmer;
overlaplen = smallKmer;
}
#endif
fprintf ( stderr, "Kmer size: %d.\n", overlaplen );
time ( &time_bef );
ctg_short = overlaplen + 2;
fprintf ( stderr, "Contig length cutoff: %d.\n", ctg_short );
prlContig2nodes ( graphfile, ctg_short );
time ( &time_aft );
fprintf ( stderr, "Time spent on graph construction: %ds.\n\n", ( int ) ( time_aft - time_bef ) );
//map long read (asm_flags=4) to edge one by one
time ( &time_bef );
prlLongRead2Ctg ( shortrdsfile, graphfile );
time ( &time_aft );
fprintf ( stderr, "Time spent on aligning long reads: %ds.\n\n", ( int ) ( time_aft - time_bef ) );
//map read to edge one by one
time ( &time_bef );
prlRead2Ctg ( shortrdsfile, graphfile );
time ( &time_aft );
fprintf ( stderr, "Time spent on aligning reads: %ds.\n\n", ( int ) ( time_aft - time_bef ) );
free_Sets ( KmerSets, thrd_num );
time ( &stop_t );
fprintf ( stderr, "Overall time spent on alignment: %dm.\n\n", ( int ) ( stop_t - start_t ) / 60 );
return 0;
}