ComputeLibStats

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ComputeLibStats
Function Statistics
Phase Assembly
Standard CLAs PRE, DATA, RUN, SUBDIR, GDB, NO_HEADER
Special CLAs LIBSTATS_DIR, USE_UNTRIMMED_LENGTHS, GENERATE_LENGTHS_FILES, USE_PLATES, UPDATE_PAIRTO_FILE, min_inserts_observed_in_plate, min_percent_plates_observed, min_percent_inserts_observed, min_score_for_cluster, min_plates_in_cluster
Source location ARACHNE_DIR/assemble
For the post-processing module, see ComputeLibraryClusters.

ComputeLibStats is a module that re-estimates insert separations and deviations based on read placements in an assembly. This may be necessary because the insert sizes given in input libraries are given with large uncertainties and may be incorrect. After placing the reads, the insert sizes can be computed to greater accuracy.

ComputeLibStats is run by Assemblez if the flag COMPUTE_LIB_STATS is set to True. It writes most of its output to the lib_stats directory, which is used by ComputeLibraryClusters.

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