Learn how easy it is to sync an existing GitHub or Google Code repo to a SourceForge project! See Demo

Close

#22 typo: agressive

open
nobody
None
5
2012-05-02
2012-05-02
No

There is a consistent typo in the way aggressive is spelt. Currently it is spelt with 1 g (agressive) in most places:

[nwatson-haigh@awrivm1 amos]$ fgrep -iR agressive .
./src/Bambus/Bundler/OrientContigs.cc: bool doAgressiveScaffolding;
./src/Bambus/Bundler/OrientContigs.cc: "OrientContigs -b[ank] <bank_name> [-all] [-noreduce] [-agressive] [-redundancy minLinks] [-repeats fileName] [-skip]\n"
./src/Bambus/Bundler/OrientContigs.cc: "The -agressive option will not mark edges that move a contig more than 3 STDEVS away as bad and will try to reconcile the positions\n"
./src/Bambus/Bundler/OrientContigs.cc: {"agressive", 0, 0, 'A'},
./src/Bambus/Bundler/OrientContigs.cc: globals.doAgressiveScaffolding = false;
./src/Bambus/Bundler/OrientContigs.cc: globals.doAgressiveScaffolding = true;
./src/Bambus/Bundler/OrientContigs.cc: cerr << "AgressiveScf = \t" << globals.doAgressiveScaffolding << endl;
./src/Bambus/Bundler/OrientContigs.cc: if (globals.doAgressiveScaffolding == true) {
Binary file ./src/Bambus/Bundler/MarkRepeats matches
Binary file ./src/Bambus/Bundler/OrientContigs.o matches
Binary file ./src/Bambus/Bundler/OrientContigs matches
Binary file ./src/Bambus/Bundler/MarkRepeats-MarkRepeats.o matches
./src/Bambus/Bundler/MarkRepeats.cc: bool doAgressiveRepeatFinding;
./src/Bambus/Bundler/MarkRepeats.cc: "MarkRepeats -b[ank] <bank_name> [-agressive] [-redundancy] [-noPathRepeats] [-noCoverageRepeats]\n"
./src/Bambus/Bundler/MarkRepeats.cc: {"agressive", 0, 0, 'R'},
./src/Bambus/Bundler/MarkRepeats.cc: globals.doAgressiveRepeatFinding = false;
./src/Bambus/Bundler/MarkRepeats.cc: globals.doAgressiveRepeatFinding = true;
./src/Bambus/Bundler/MarkRepeats.cc: cerr << "AgressiveRepats = \t" << globals.doAgressiveRepeatFinding << endl;
./src/Bambus/Bundler/MarkRepeats.cc: } else if (globals.doAgressiveRepeatFinding == true && globalCov <= MAX_REPEAT_COV && (*j)->getUngappedLength() < MAX_REPEAT_SIZE) {
./src/Bambus/Bundler/MarkRepeats.cc: if (globals.debug > 1) cerr << "AGRESSIVE REPEAT" << cov << " IS TOO LOW" << endl;

Discussion

    • summary: type: agressive --> typo: agressive