From 75b61da3ab27712bd96690b1e52a4c3c12788d49 Mon Sep 17 00:00:00 2001
From: Calvin Morrison <mutantturkey@gmail.com>
Date: Mon, 14 Apr 2014 13:15:47 -0400
Subject: merge

---
 Makefile         | 15 ++++++++++-----
 kmer_locations.c |  5 +++--
 2 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/Makefile b/Makefile
index 745ee16..6e3f42f 100644
--- a/Makefile
+++ b/Makefile
@@ -1,9 +1,10 @@
 VERSION=\"0.0.5\"
 CC = g++
 CFLAGS = -O3 -s -march=native -Wall -Wextra -DVERSION=$(VERSION) -std=c++11
-DESTDIR = /usr/local/
+DESTDIR = /usr/local
 
-all: libkmer.so kmer_total_count kmer_counts_per_sequence kmer_utils.o kmer_locations
+all: libkmer.so kmer_total_count kmer_counts_per_sequence kmer_utils.o \
+		 kmer_locations kmer_continuous_count
 
 kmer_utils.o: kmer_utils.c
 	$(CC) -c kmer_utils.c -O $(CFLAGS) -fPIC
@@ -23,12 +24,16 @@ kmer_continuous_count: kmer_utils.o kmer_continuous_count.c kmer_utils.h
 kmer_locations: kmer_utils.o kmer_locations.c kmer_utils.h
 	$(CC) kmer_utils.o kmer_locations.c -o kmer_locations $(CLIBS) $(CFLAGS)
 clean:
-	rm -vf kmer_locations kmer_total_count kmer_counts_per_sequence kmer_continuous_count kmer_utils.o libkmer.so
+	rm -vf kmer_total_count kmer_counts_per_sequence kmer_continuous_count \
+	kmer_utils.o libkmer.so kmer_locations
 
 debug: CFLAGS = -ggdb -Wall -Wextra -DVERSION=$(VERSION)\"-debug\" -std=c++11
 debug: all
 
 install: all
-	@cp -vf kmer_counts_per_sequence kmer_total_count kmer_continuous_count $(DESTDIR)/bin/
-	@cp -vf  libkmer.so  $(DESTDIR)/lib/
+	install kmer_counts_per_sequence $(DESTDIR)/bin
+	install kmer_total_count $(DESTDIR)/bin
+	install kmer_continuous_count $(DESTDIR)/bin
+	install kmer_locations $(DESTDIR)/bin
+	cp -vf  libkmer.so  $(DESTDIR)/lib/
 
diff --git a/kmer_locations.c b/kmer_locations.c
index 56bf934..a6a2dc9 100644
--- a/kmer_locations.c
+++ b/kmer_locations.c
@@ -223,7 +223,6 @@ int main(int argc, char **argv) {
 	}
 
 
-	unsigned long long sequence = 0;
 	unsigned long long global_position = 0;
 
 	while ((read = getdelim(&line, &len, '>', fh)) != -1) {
@@ -241,6 +240,9 @@ int main(int argc, char **argv) {
 		// strip out all other newlines to handle multiline sequences
 		size_t seq_length = strnstrip(seq, '\n', strlen(seq));
 
+		if(seq[seq_length - 1] == '>') 
+			seq_length --;
+
 		for(k = 0; k < seq_length; k++) {
 			seq[k] = alpha[(int)seq[k]];
 		}
@@ -266,7 +268,6 @@ int main(int argc, char **argv) {
 		if(seq_length != 0) {
 			seq_length--;
 		}
-		sequence++;
 		global_position += seq_length;
 	}
 
-- 
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