@@ -452,6 +452,26 @@ sub mhapConfigure ($$$) {
452 452
print F "echo \"\"\n";
453 453
print F "\n";
454 454
print F "if [ ! -e \$outPath/\$qry.mhap ] ; then\n";
455 + 456 +
if (getGlobal("${tag}mhapPipe")) {
457 +
print F " # Make a fifo so we can check return status on both\n";
458 +
print F " # mhap and mhapConvert, and still pipe results so we\n";
459 +
print F " # stop filling up disks.\n";
460 +
print F " rm -f \$qry-pipe\n";
461 +
print F " mkfifo \$qry-pipe\n";
462 +
print F "\n";
463 +
print F " # Start up the consumer.\n";
464 +
print F " \$bin/mhapConvert \\\n";
465 +
print F " -S ../../$asm.seqStore \\\n";
466 +
print F " -o ./results/\$qry.mhap.ovb.WORKING \\\n";
467 +
print F " -minlength ", getGlobal("minOverlapLength"), " \\\n";
468 +
print F " \$qry-pipe \\\n";
469 +
print F " && \\\n";
470 +
print F " touch ./results/\$qry.mcvt.success &\n";
471 +
print F "\n";
472 +
}
473 + 474 +
print F " # Start up the producer.\n";
455 475
print F " $javaPath $javaOpt -XX:ParallelGCThreads=", getGlobal("${tag}mhapThreads"), " -server -Xms", $javaMemory, "m -Xmx", $javaMemory, "m \\\n";
456 476
print F " -jar $cygA \$bin/../share/java/classes/mhap-" . getGlobal("${tag}MhapVersion") . ".jar $cygB \\\n";
457 477
print F " --repeat-weight 0.9 --repeat-idf-scale 10 -k $merSize \\\n";
@@ -469,30 +489,49 @@ sub mhapConfigure ($$$) {
469 489
print F " " . getGlobal("${tag}MhapOptions") . " \\\n" if (defined(getGlobal("${tag}MhapOptions")));
470 490
print F " -s $cygA ./blocks/\$blk.dat \$slf $cygB \\\n";
471 491
print F " -q $cygA queries/\$qry $cygB \\\n";
472 -
print F " > \$outPath/\$qry.mhap.WORKING \\\n";
473 -
print F " && \\\n";
474 -
print F " mv -f \$outPath/\$qry.mhap.WORKING \$outPath/\$qry.mhap\n";
475 -
print F "fi\n";
476 -
print F "\n";
477 492 478 -
print F "if [ -e \$outPath/\$qry.mhap -a \\\n";
479 -
print F " ! -e ./results/\$qry.ovb ] ; then\n";
480 -
print F " \$bin/mhapConvert \\\n";
481 -
print F " -S ../../$asm.seqStore \\\n";
482 -
print F " -o ./results/\$qry.mhap.ovb.WORKING \\\n";
483 -
print F " -minlength ", getGlobal("minOverlapLength"), " \\\n";
484 -
print F " \$outPath/\$qry.mhap \\\n";
485 -
print F " && \\\n";
486 -
print F " mv ./results/\$qry.mhap.ovb.WORKING ./results/\$qry.mhap.ovb\n";
487 -
print F "fi\n";
488 -
print F "\n";
493 +
if (getGlobal("${tag}mhapPipe")) {
494 +
print F " > \$qry-pipe \\\n";
495 +
print F " && \\\n";
496 +
print F " touch ./results/\$qry.mhap.success\n";
497 +
print F "\n";
498 +
print F " # Now that they're done, check status.\n";
499 +
print F " if [ -e ./results/\$qry.mhap.success -a -e ./results/\$qry.mcvt.success ] ; then\n";
500 +
print F " mv ./results/\$qry.mhap.ovb.WORKING ./results/\$qry.mhap.ovb\n";
501 +
print F " rm -f ./results/\$qry.mhap.success\n";
502 +
print F " rm -f ./results/\$qry.mcvt.success\n";
503 +
print F " fi\n";
504 +
print F "\n";
505 +
print F " # And destroy the pipe.\n";
506 +
print F " rm -f \$qry-pipe\n";
507 +
print F "fi\n";
508 +
print F "\n";
509 +
} else {
510 +
print F " > \$outPath/\$qry.mhap.WORKING \\\n";
511 +
print F " && \\\n";
512 +
print F " mv -f \$outPath/\$qry.mhap.WORKING \$outPath/\$qry.mhap\n";
513 +
print F "fi\n";
514 +
print F "\n";
489 515 490 -
if (getGlobal('purgeOverlaps') ne "never") {
491 516
print F "if [ -e \$outPath/\$qry.mhap -a \\\n";
492 -
print F " -e ./results/\$qry.mhap.ovb ] ; then\n";
493 -
print F " rm -f \$outPath/\$qry.mhap\n";
517 +
print F " ! -e ./results/\$qry.ovb ] ; then\n";
518 +
print F " \$bin/mhapConvert \\\n";
519 +
print F " -S ../../$asm.seqStore \\\n";
520 +
print F " -o ./results/\$qry.mhap.ovb.WORKING \\\n";
521 +
print F " -minlength ", getGlobal("minOverlapLength"), " \\\n";
522 +
print F " \$outPath/\$qry.mhap \\\n";
523 +
print F " && \\\n";
524 +
print F " mv ./results/\$qry.mhap.ovb.WORKING ./results/\$qry.mhap.ovb\n";
494 525
print F "fi\n";
495 526
print F "\n";
527 + 528 +
if (getGlobal('purgeOverlaps') ne "never") {
529 +
print F "if [ -e \$outPath/\$qry.mhap -a \\\n";
530 +
print F " -e ./results/\$qry.mhap.ovb ] ; then\n";
531 +
print F " rm -f \$outPath/\$qry.mhap\n";
532 +
print F "fi\n";
533 +
print F "\n";
534 +
}
496 535
}
497 536 498 537
if (getGlobal("${tag}ReAlign") eq "1") {
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