From 2c038ba630c14c7030186c64e9eb92761ddcba74 Mon Sep 17 00:00:00 2001 From: Calvin Morrison Date: Thu, 6 Mar 2014 17:05:40 -0500 Subject: add kmer_continuous_count this tool will count continuously, instead of line by line. The way that this works out is something like this: test.fa > header 1 AAAAATTTTT > header 2 GGGGGAAAAA counting 6 mers, the program will count TTTGGG, TTGGGG, TGGGGG, like there was no header seperating them. This can be useful for certain tyeps of processing, like when the sequences are continuous from a genome. initial commit --- Makefile | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'Makefile') diff --git a/Makefile b/Makefile index c929cfd..dc47796 100644 --- a/Makefile +++ b/Makefile @@ -4,7 +4,7 @@ CFLAGS = -O3 -s -mtune=native -Wall -DVERSION=$(VERSION) -Wextra DESTDIR = /usr/local/ -all: libkmer.o libkmer.so kmer_total_count kmer_counts_per_sequence +all: libkmer.o libkmer.so kmer_total_count kmer_counts_per_sequence kmer_continuous_count libkmer.o: kmer_utils.c $(CC) -c kmer_utils.c -o libkmer.o $(CFLAGS) -fPIC @@ -14,9 +14,11 @@ kmer_total_count: libkmer.o kmer_total_count.c kmer_utils.h $(CC) libkmer.o kmer_total_count.c -o kmer_total_count $(CLIBS) $(CFLAGS) kmer_counts_per_sequence: libkmer.o kmer_counts_per_sequence.c kmer_utils.h $(CC) libkmer.o kmer_counts_per_sequence.c -o kmer_counts_per_sequence $(CLIBS) $(CFLAGS) +kmer_continuous_count: libkmer.o kmer_continuous_count.c kmer_utils.h + $(CC) libkmer.o kmer_continuous_count.c -o kmer_continuous_count $(CLIBS) $(CFLAGS) clean: - rm -vf kmer_total_count kmer_counts_per_sequence libkmer.so libkmer.o + rm -vf kmer_total_count kmer_counts_per_sequence kmer_continuous_count libkmer.so libkmer.o debug: CFLAGS = -ggdb -Wall -Wextra -DVERSION=$(VERSION)\"-debug\" debug: all -- cgit v1.2.3