Lines Matching refs:getGlobal
84 sub getGlobal ($) { subroutine
103 if (!defined(getGlobal($var))) {
391 my $errors = getGlobal("errors");
526 if ((getGlobal("corOverlapper") eq "mhap") ||
527 (getGlobal("obtOverlapper") eq "mhap") ||
528 (getGlobal("utgOverlapper") eq "mhap")) {
536 if ((getGlobal("corOverlapper") eq "ovl") ||
537 (getGlobal("obtOverlapper") eq "ovl") ||
538 (getGlobal("utgOverlapper") eq "ovl")) {
546 if ((getGlobal("corOverlapper") eq "minimap") ||
547 (getGlobal("obtOverlapper") eq "minimap") ||
548 (getGlobal("utgOverlapper") eq "minimap")) {
577 my $val = getGlobal($var);
595 my $VAL = getGlobal($var);
1061 return if ((getGlobal("corOverlapper") ne "mhap") &&
1062 (getGlobal("obtOverlapper") ne "mhap") &&
1063 (getGlobal("utgOverlapper") ne "mhap"));
1065 my $java = getGlobal("java");
1066 my $javaUse64Bit = getGlobal("javaUse64Bit");
1109 setGlobal("javaUse64Bit", 0) if (!defined(getGlobal("javaUse64Bit")));
1121 …print STDERR (defined(getGlobal("javaUse64Bit")) && getGlobal("javaUse64Bit") == 1) ? " with " : "…
1129 my $minimap = getGlobal("minimap");
1132 return if ((getGlobal("corOverlapper") ne "minimap") &&
1133 (getGlobal("obtOverlapper") ne "minimap") &&
1134 (getGlobal("utgOverlapper") ne "minimap"));
1163 my $gnuplot = getGlobal("gnuplot");
1164 my $format = getGlobal("gnuplotImageFormat");
1395 setGlobal("genomeSize", adjustGenomeSize(getGlobal("genomeSize")));
1397 setGlobal("minMemory", adjustMemoryValue(getGlobal("minMemory")));
1398 setGlobal("maxMemory", adjustMemoryValue(getGlobal("maxMemory")));
1400 setGlobal("executiveMemory", adjustMemoryValue(getGlobal("executiveMemory")));
1402 …if (getGlobal("executiveMemory") < getGlobal("minMemory")) { # Silently bump up execMemory to m…
1403 setGlobal("executiveMemory", getGlobal("minMemory")); # if needed.
1410 my $gs = getGlobal("genomeSize");
1422 if (exists($ENV{getGlobal("gridEngineTaskID")})) {
1423 my $ja = $ENV{getGlobal("gridEngineTaskID")};
1428 …print STDERR "-- I appear to be task $ja in a job array, unsetting ", getGlobal("gridEngineTaskID"…
1431 undef $ENV{getGlobal("gridEngineTaskID")};
1438 if (!defined(getGlobal($var))) {
1440 elsif (getGlobal($var) !~ m/^[.-0123456789]+$/) {
1441 …addCommandLineError("ERROR: Invalid '$var' specified (" . getGlobal("$var") . "); must be numeric…
1443 elsif ((getGlobal($var) < 0.0) || (getGlobal($var) > 1.0)) {
1444 …addCommandLineError("ERROR: Invalid '$var' specified (" . getGlobal("$var") . "); must be at leas…
1449 if (!defined(getGlobal($var))) {
1451 elsif (getGlobal($var) !~ m/^[.-0123456789]+$/) {
1452 …addCommandLineError("ERROR: Invalid '$var' specified (" . getGlobal("$var") . "); must be numeric…
1454 elsif ((getGlobal($var) < 0.0) || (getGlobal($var) > 1.0)) {
1455 …addCommandLineError("ERROR: Invalid '$var' specified (" . getGlobal("$var") . "); must be at leas…
1460 if (!defined(getGlobal($var))) {
1462 elsif (getGlobal($var) !~ m/^[0123456789]+$/) {
1463 …addCommandLineError("ERROR: Invalid '$var' specified (" . getGlobal("$var") . "); must be an inte…
1465 elsif (getGlobal($var) < 2) {
1466 …addCommandLineError("ERROR: Invalid '$var' specified (" . getGlobal("$var") . "); must be at leas…
1470 if (getGlobal("minReadLength") < getGlobal("minOverlapLength")) {
1471 my $mr = getGlobal("minReadLength");
1472 my $mo = getGlobal("minOverlapLength");
1478 if (!defined(getGlobal($var))) {
1481 elsif (getGlobal($var) =~ m/all/i) {
1484 elsif (getGlobal($var) !~ m/^[.-0123456789]+$/) {
1485 …addCommandLineError("ERROR: Invalid '$var' specified (" . getGlobal("$var") . "); must be numeric…
1487 elsif (getGlobal($var) < 1.0) {
1488 …addCommandLineError("ERROR: Invalid '$var' specified (" . getGlobal("$var") . "); must be at leas…
1493 if (!defined(getGlobal($var))) {
1496 elsif (getGlobal($var) =~ m/^(\d*\.*\d*)(x*)$/) {
1498 …addCommandLineError("ERROR: Invalid '$var' specified (" . getGlobal("$var") . "); must be at leas…
1502 …addCommandLineError("ERROR: Invalid '$var' specified (" . getGlobal("$var") . "); must be numeric…
1507 … setGlobal("utgGraphDeviation", 12) if $var eq "utgGraphDeviation" && !defined(getGlobal($var));
1508 … setGlobal("utgRepeatDeviation", 1) if $var eq "utgRepeatDeviation" && !defined(getGlobal($var));
1510 if (!defined(getGlobal($var))) {
1513 elsif (getGlobal($var) !~ m/^[.-0123456789]+$/) {
1514 …addCommandLineError("ERROR: Invalid '$var' specified (" . getGlobal("$var") . "); must be numeric…
1516 elsif (getGlobal($var) < 0.0) {
1517 …addCommandLineError("ERROR: Invalid '$var' specified (" . getGlobal("$var") . "); must be at leas…
1521 if ((getGlobal("utgChimeraType") ne "none") &&
1522 (getGlobal("utgChimeraType") ne "chimer") &&
1523 (getGlobal("utgChimeraType") ne "uncovered") &&
1524 (getGlobal("utgChimeraType") ne "deadend")) {
1525 …addCommandLineError("ERROR: Invalid 'utgChimeraType' specified (" . getGlobal("utgChimeraType") .…
1533 if ((getGlobal("${tag}Overlapper") ne "mhap") &&
1534 (getGlobal("${tag}Overlapper") ne "ovl") &&
1535 (getGlobal("${tag}Overlapper") ne "minimap")) {
1536 …addCommandLineError("ERROR: Invalid '${tag}Overlapper' specified (" . getGlobal("${tag}Overlapper…
1541 if (getGlobal("${tag}MhapSensitivity") eq "fast") {
1545 if ((getGlobal("${tag}MhapSensitivity") ne undef) &&
1546 (getGlobal("${tag}MhapSensitivity") ne "low") &&
1547 (getGlobal("${tag}MhapSensitivity") ne "normal") &&
1548 (getGlobal("${tag}MhapSensitivity") ne "high")) {
1549 …addCommandLineError("ERROR: Invalid '${tag}MhapSensitivity' specified (" . getGlobal("${tag}MhapS…
1553 if (getGlobal("unitigger") ne "bogart") {
1554 …addCommandLineError("ERROR: Invalid 'unitigger' specified (" . getGlobal("unitigger") . "); must …
1557 if ((getGlobal("corConsensus") ne "falcon")) {
1558 …addCommandLineError("ERROR: Invalid 'corConsensus' specified (" . getGlobal("corConsensus") . ");…
1561 if ((getGlobal("cnsConsensus") ne "quick") &&
1562 (getGlobal("cnsConsensus") ne "pbdagcon") &&
1563 (getGlobal("cnsConsensus") ne "utgcns")) {
1564 …addCommandLineError("ERROR: Invalid 'cnsConsensus' specified (" . getGlobal("cnsConsensus") . ");…
1567 if (!defined(getGlobal("maxInputCoverage"))) {
1570 if (getGlobal("maxInputCoverage") eq "all") {
1573 …if ((getGlobal("maxInputCoverage") > 0) && (getGlobal("maxInputCoverage") < getGlobal("minInputCov…
1574 my $minc = getGlobal("minInputCoverage");
1575 my $maxc = getGlobal("maxInputCoverage");
1579 …if ((getGlobal("maxInputCoverage") > 0) && (getGlobal("maxInputCoverage") < getGlobal("stopOnLowCo…
1580 my $minc = getGlobal("stopOnLowCoverage");
1581 my $maxc = getGlobal("maxInputCoverage");
1586 if ((getGlobal("saveOverlaps") ne "0") &&
1587 (getGlobal("saveOverlaps") ne "1")) {
1588 …addCommandLineError("ERROR: Invalid 'saveOverlaps' specified (" . getGlobal("saveOverlaps") . ");…
1591 if ((getGlobal("purgeOverlaps") eq "0") ||
1592 (getGlobal("purgeOverlaps") eq "no")) {
1596 if ((getGlobal("purgeOverlaps") eq "1") ||
1597 (getGlobal("purgeOverlaps") eq "yes")) {
1601 if ((getGlobal("purgeOverlaps") ne "never") &&
1602 (getGlobal("purgeOverlaps") ne "normal") &&
1603 (getGlobal("purgeOverlaps") ne "aggressive") &&
1604 (getGlobal("purgeOverlaps") ne "dangerous")) {
1605 …addCommandLineError("ERROR: Invalid 'purgeOverlaps' specified (" . getGlobal("purgeOverlaps") . "…
1608 if ((getGlobal("corFilter") ne "quick") &&
1609 (getGlobal("corFilter") ne "expensive") &&
1610 (getGlobal("corFilter") ne "none")) {
1611 …addCommandLineError("ERROR: Invalid 'corFilter' specified (" . getGlobal("corFilter") . "); must …
1615 if ((getGlobal("useGrid") ne "0") &&
1616 (getGlobal("useGrid") ne "1") &&
1617 (getGlobal("useGrid") ne "remote")) {
1618 …addCommandLineError("ERROR: Invalid 'useGrid' specified (" . getGlobal("useGrid") . "); must be '…
1622 if (defined(getGlobal("stopAfter"))) {
1624 my $st = getGlobal("stopAfter");
1630 …my $failureString = "ERROR: Invalid stopAfter specified (" . getGlobal("stopAfter") . "); must be…
1667 my @v = split '\s+', getGlobal("contigFilter");