Commit d0f7cc98 authored by Martin Frith's avatar Martin Frith
Browse files

lastal: increase batch size with multi-thread

parent 1705b461
......@@ -172,7 +172,7 @@ Miscellaneous options (default settings):\n\
-C: omit gapless alignments in >= C others with > score-per-length (off)\n\
-P: number of parallel threads ("
+ stringify(numOfThreads) + ")\n\
-i: query batch size (8 KiB, unless there is > 1 thread or lastdb volume)\n\
-i: query batch size (64M if multi-volume, else 32M if multi-thread, else 8K)\n\
-M: find minimum-difference alignments (faster but cruder)\n\
-T: type of alignment: 0=local, 1=overlap ("
+ stringify(globality) + ")\n\
......@@ -524,7 +524,10 @@ void LastalArguments::setDefaultsFromAlphabet( bool isDna, bool isProtein,
else if( outputType == 0 )
batchSize = 0x1000000; // 16 Mbytes
else if( !isVolumes )
batchSize = 0x800000; // 8 Mbytes
batchSize = 0x2000000; // 32 Mbytes
// 32 Mbytes gave quite good load-balancing when aligning human
// nanopore reads with 16 threads. Sometimes 64M (and even 128M)
// was better. With WindowMasker, smaller batches were fine.
else if( inputFormat == sequenceFormat::prb )
batchSize = 0x2000000; // 32 Mbytes (?)
else
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment