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port physlr split-minimizers to c++ (#145)
* port physlr split-minimizers to c++ * physlr-split-minimizers.cc: refactor arg parser * physlr-split-minimizers.cc: fix clang-tidy * physlr-split-minimizers.cc: use auto * physlr-split-minimizers.cc: update comments * physlr-split-minimizers.cc: add print memoryUsage to functions * physlr-split-minimizers.cc: update regex * physlr-split-minimizers.cc: use robin map * physlr-split-minimizers.cc: remove no minimizer warning for speed * physlr-split-minimizers: add unit test * physlr-make: update physlr-make split minimizers rule * physlr-split-minimizers.cc: report splitting time * physlr-split-minimizers.cc: remove critical brace * physlr-split-minimizers.cc: update log message
1 parent accf43c commit a838772

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‎bin/physlr-make‎

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# Split the minimizers to molecules
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%.overlap.m$m.mol.mol2-bcs.split.tsv: %.overlap.m$m.mol.mol2-bcs.tsv %.tsv
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$(time) $(python) $(bin)/physlr split-minimizers -t$t -V$V $< $*.tsv >$@
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$(time) $(physlr_path)/src/physlr-split-minimizers -t$t $< $*.tsv >$@
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# Split the reads into molecules
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%.split.fq.gz: $(lr).fq.gz %.split.tsv $(lr).k$k-w$w.physlr.tsv

‎src/Makefile‎

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@@ -2,12 +2,12 @@ CXXFLAGS=-g -O3 -Wall -Werror -Wno-error=unknown-pragmas -std=c++11 -pthread -I.
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LDLIBS=-lz
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PREFIX=$(HOME)/.local
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.PHONY: all clean check install lint clang-format clang-tidy fix check-physlr-index-fasta check-physlr-index-pos-fasta check-physlr-index-fastq check-physlr-filter-barcodes check-physlr-filter-bxmx-first check-physlr-filter-bxmx-second check-physlr-index-stLFR check-physlr-index-stLFR-10X check-physlr-makebf check-physlr-overlap
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.PHONY: all clean check install lint clang-format clang-tidy fix check-physlr-index-fasta check-physlr-index-pos-fasta check-physlr-index-fastq check-physlr-filter-barcodes check-physlr-filter-bxmx-first check-physlr-filter-bxmx-second check-physlr-index-stLFR check-physlr-index-stLFR-10X check-physlr-makebf check-physlr-overlap check-physlr-split-minimizers
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all: physlr-indexlr physlr-filter-barcodes physlr-overlap physlr-filter-bxmx physlr-makebf physlr-molecules
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all: physlr-indexlr physlr-filter-barcodes physlr-overlap physlr-filter-bxmx physlr-makebf physlr-molecules physlr-split-minimizers
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clean:
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rm -f physlr-indexlr physlr-filter-barcodes physlr-filter-bxmx physlr-overlap physlr-makebf physlr-molecules
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rm -f physlr-indexlr physlr-filter-barcodes physlr-filter-bxmx physlr-overlap physlr-makebf physlr-molecules physlr-split-minimizers
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# Check the C++ source code for errors.
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lint: clang-format clang-tidy
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check-physlr-molecules: all
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./physlr-molecules -s bc data/tiny.mol.input.tsv | diff -q - data/tiny.mol.tsv.good
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install: physlr-indexlr physlr-filter-barcodes physlr-overlap physlr-filter-bxmx physlr-makebf physlr-molecules
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check-physlr-split-minimizers: all
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./physlr-split-minimizers -t4 data/tiny.split-minimizers.mol.mol2-bcs.tsv data/tiny.split-minimizers.physlr.tsv | sort |diff -q - data/tiny.split-minimizers.mol.mol2-bcs.split.tsv.good
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install: physlr-indexlr physlr-filter-barcodes physlr-overlap physlr-filter-bxmx physlr-makebf physlr-molecules physlr-split-minimizers
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install -d $(DESTDIR)$(PREFIX)/bin
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install $^ $(DESTDIR)$(PREFIX)/bin

‎src/data/tiny.split-minimizers.mol.mol2-bcs.split.tsv.good‎

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‎src/data/tiny.split-minimizers.mol.mol2-bcs.tsv‎

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‎src/data/tiny.split-minimizers.physlr.tsv‎

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