FixLocations

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FixLocations
Function Cleanup
Phase Assembly
Standard CLAs PRE, DATA, RUN, SUBDIR, GDB, NO_HEADER
Special CLAs ONE_SUPER, ID, ONE_CONTIG, CONTIG_ID, MANY_CONTIGS, LOAD_ALL, MODIFY, HISTOGRAM, USE_FASTB, VERBOSE, popUnalignableReads, useAdjustedTrims, quickCheck, UnmergeLocsForAssemblez
Source location ARACHNE_DIR/assemble

FixLocations is a module that fine-tunes ReadLocation objects by recalculating alignments between reads and contigs. When run with MODIFY=True, it creates the file mergedcontigs.pma. Any module that relies heavily on alignments, such as CreateAceFile, should not be run without first running FixLocations.

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