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Only in old/bin: build_bithash
Only in old/bin: correct
Only in old/bin: count-kmers
Only in old/bin: count-qmers
diff -rup old/bin/quake.py new/bin/quake.py
--- old/bin/quake.py 2012-06-22 22:58:49.675854704 -0400
+++ new/bin/quake.py 2012-06-22 22:58:34.139187280 -0400
@@ -117,14 +117,14 @@ def main():
correct_options = make_cor_opts(options)
if options.model_gc:
# run correct C++ code
- p = subprocess.Popen('%s/correct %s %s -m %s -a cutoffs.gc.txt -q %d' % (quake_dir, correct_options, reads_str, ctsf, quality_scale), shell=True)
+ p = subprocess.Popen('%s/quake-correct %s %s -m %s -a cutoffs.gc.txt -q %d' % (quake_dir, correct_options, reads_str, ctsf, quality_scale), shell=True)
os.waitpid(p.pid, 0)
else:
cutoff = get_cutoff()
# run correct C++ code
- p = subprocess.Popen('%s/correct %s %s -m %s -c %s -q %d' % (quake_dir, correct_options, reads_str, ctsf, cutoff, quality_scale), shell=True)
+ p = subprocess.Popen('%s/quake-correct %s %s -m %s -c %s -q %d' % (quake_dir, correct_options, reads_str, ctsf, cutoff, quality_scale), shell=True)
os.waitpid(p.pid, 0)
@@ -146,9 +146,9 @@ def count_kmers(readsf, reads_listf, k,
# count
if ctsf[-4:] == 'qcts':
- p = subprocess.Popen('cat %s | %s/count-qmers -k %d -q %d > %s' % (' '.join(fq_files), quake_dir, k, quality_scale, ctsf), shell=True)
+ p = subprocess.Popen('cat %s | %s/quake-count-qmers -k %d -q %d > %s' % (' '.join(fq_files), quake_dir, k, quality_scale, ctsf), shell=True)
else:
- p = subprocess.Popen('cat %s | %s/count-kmers -k %d > %s' % (' '.join(fq_files), quake_dir, k, ctsf), shell=True)
+ p = subprocess.Popen('cat %s | %s/quake-count-kmers -k %d > %s' % (' '.join(fq_files), quake_dir, k, ctsf), shell=True)
os.waitpid(p.pid, 0)
diff -rup old/src/Makefile new/src/Makefile
--- old/src/Makefile 2012-06-22 22:58:58.809188485 -0400
+++ new/src/Makefile 2012-06-22 23:06:00.979209086 -0400
@@ -2,9 +2,9 @@ CXX := g++
CXXFLAGS := $(CXXFLAGS) -fopenmp -I.
LDFLAGS := -L. -lgzstream -lz
#INCLUDEDIR=
-EXE_FILES := correct count-kmers count-qmers \
- count_qmers reduce-kmers reduce-qmers \
- trim build_bithash correct_stats
+EXE_FILES := quake-correct quake-count-kmers quake-count-qmers \
+ quake-count-qmers2 quake-reduce-kmers quake-reduce-qmers \
+ quake-trim quake-build-bithash quake-correct-stats
.PHONY: all clean
all: $(EXE_FILES)
@@ -12,35 +12,36 @@ all: $(EXE_FILES)
clean:
-rm $(EXE_FILES) *.o
-correct: correct.cpp Read.o bithash.o edit.o libgzstream.a
- $(CXX) $(CXXFLAGS) correct.cpp Read.o bithash.o edit.o -o correct $(LDFLAGS)
+quake-correct: correct.cpp Read.o bithash.o edit.o libgzstream.a
+ $(CXX) $(CXXFLAGS) correct.cpp Read.o bithash.o edit.o -o $@ $(LDFLAGS)
-count-kmers: count-kmers.cpp count.o
- $(CXX) $(CXXFLAGS) count-kmers.cpp count.o -o count-kmers
+quake-count-kmers: count-kmers.cpp count.o
+ $(CXX) $(CXXFLAGS) count-kmers.cpp count.o -o $@
-count-qmers: count-qmers.cpp count.o
- $(CXX) $(CXXFLAGS) count-qmers.cpp count.o -o count-qmers
+quake-count-qmers: count-qmers.cpp count.o
+ $(CXX) $(CXXFLAGS) count-qmers.cpp count.o -o $@
-count_qmers: count_qmers.cpp count.o qmer_hash.o
- $(CXX) $(CXXFLAGS) -o count_qmers count_qmers.cpp count.o qmer_hash.o
+quake-count-qmers2: count_qmers.cpp count.o qmer_hash.o
+ $(CXX) $(CXXFLAGS) -o $@ count_qmers.cpp count.o qmer_hash.o
-qmer_hash.o: qmer_hash.cpp qmer_hash.h
- $(CXX) $(CXXFLAGS) -c qmer_hash.cpp
-reduce-kmers: reduce-kmers.cpp
- $(CXX) $(CXXFLAGS) reduce-kmers.cpp -o reduce-kmers
+quake-reduce-kmers: reduce-kmers.cpp
+ $(CXX) $(CXXFLAGS) reduce-kmers.cpp -o $@
+
+quake-reduce-qmers: reduce-qmers.cpp
+ $(CXX) $(CXXFLAGS) reduce-qmers.cpp -o $@
-reduce-qmers: reduce-qmers.cpp
- $(CXX) $(CXXFLAGS) reduce-qmers.cpp -o reduce-qmers
+quake-trim: trim.cpp Read.o bithash.o edit.o libgzstream.a
+ $(CXX) $(CXXFLAGS) trim.cpp Read.o bithash.o edit.o -o $@ $(LDFLAGS)
-trim: trim.cpp Read.o bithash.o edit.o libgzstream.a
- $(CXX) $(CXXFLAGS) trim.cpp Read.o bithash.o edit.o -o trim $(LDFLAGS)
+quake-build-bithash: build_bithash.cpp bithash.o
+ $(CXX) $(CXXFLAGS) build_bithash.cpp bithash.o -o $@
-build_bithash: build_bithash.cpp bithash.o
- $(CXX) $(CXXFLAGS) build_bithash.cpp bithash.o -o build_bithash
+quake-correct-stats: stats.cpp
+ $(CXX) $(CXXFLAGS) stats.cpp -o $@
-correct_stats: stats.cpp
- $(CXX) $(CXXFLAGS) stats.cpp -o correct_stats
+qmer_hash.o: qmer_hash.cpp qmer_hash.h
+ $(CXX) $(CXXFLAGS) -c qmer_hash.cpp
Read.o: Read.cpp Read.h bithash.o
$(CXX) $(CXXFLAGS) -c Read.cpp
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