From 3da54df39fa6aeb4f3f861d0d6a0af91671f9492 Mon Sep 17 00:00:00 2001
From: Mart Lubbers <mart@martlubbers.net>
Date: Tue, 3 Feb 2015 21:47:26 +0100
Subject: [PATCH] final final final mart

---
 .../sws1-s4109503-s4202015/exercise1/commands |  2 +-
 .../sws1-s4109503-s4202015/exercise2/Makefile |  2 +-
 .../exercise2/parsegenome.c                   | 31 ++++++++++---------
 3 files changed, 18 insertions(+), 17 deletions(-)

diff --git a/ass1/mart/sws1-s4109503-s4202015/exercise1/commands b/ass1/mart/sws1-s4109503-s4202015/exercise1/commands
index 8748d46..d98ef31 100644
--- a/ass1/mart/sws1-s4109503-s4202015/exercise1/commands
+++ b/ass1/mart/sws1-s4109503-s4202015/exercise1/commands
@@ -1,4 +1,4 @@
-mkdir -p sws1-s4109503-s4202015/exercise{1,2,3}
+mkdir -p sws1-s4109503-s4202015/exercise{1,2}
 cd sws1-s4109503-s4202015
 echo -e "s4109503: Mart Lubbers\ns4202015: Chris Kamphuis" > names.txt
 du -sb | cut -f 1 > exercise1/1b.txt
diff --git a/ass1/mart/sws1-s4109503-s4202015/exercise2/Makefile b/ass1/mart/sws1-s4109503-s4202015/exercise2/Makefile
index e7ef6d1..fa18e55 100644
--- a/ass1/mart/sws1-s4109503-s4202015/exercise2/Makefile
+++ b/ass1/mart/sws1-s4109503-s4202015/exercise2/Makefile
@@ -1,5 +1,5 @@
 CC=gcc
-CFLAGS=-Wall -Wextra
+CFLAGS=-std=c99 -Wall -Wextra
 
 all: parsegenome.c
 	$(CC) $(CFLAGS) parsegenome.c -o parsegenome
diff --git a/ass1/mart/sws1-s4109503-s4202015/exercise2/parsegenome.c b/ass1/mart/sws1-s4109503-s4202015/exercise2/parsegenome.c
index d561d4f..9acb1cf 100644
--- a/ass1/mart/sws1-s4109503-s4202015/exercise2/parsegenome.c
+++ b/ass1/mart/sws1-s4109503-s4202015/exercise2/parsegenome.c
@@ -1,29 +1,30 @@
-#include <stdint.h> /* - Basically we save the 4 frequencies in a 64bit int  */
-#include <stdio.h>  /* - The polynome fits the following coordinates:        */
-#include <stdlib.h> /* (65,0), (67, 16), (71, 32), (84, 48)                  */
-#include <string.h> /* - Which is the mapping from ascii value and shiftwidth*/
-                    /* - When no input file is given assume stdin            */
+#include <stdint.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
 int main(int argc, char* argv[])
 {
+	char *alphabet = "AGTC";
 	char c;
-	char charsperline = 0;
-	short numlines = 0;
+	int charsperline = 0;
+	int numlines = 0;
 	uint64_t occs = 0;
-	FILE *f = (argc!=2 || strcmp(argv[1], "-")==0) ? stdin : fopen(argv[1], "r");
+	FILE *f = argc != 2 ? stdin : fopen(argv[1], "r");
 	if(f == NULL)
 		return 2;
-	while((c=fgetc(f)) != EOF)
+	while((c = fgetc(f)) != EOF)
 		if(c == '\n' && charsperline == 100 && numlines++ < 500)
 			charsperline = 0;
-		else if((c=='A' ||c=='C' || c=='G' || c=='T') && charsperline++<100)
-			occs += 1LL<<(char)(0.026514*c*c*c-6.049*c*c+459.96*c-11621.2);
+		else if(strchr(alphabet, c) && charsperline++ < 100)
+			occs += 1LL<<((int)(strchr(alphabet, c)-alphabet)*16);
 		else
 			break;
-	if(f != stdout)
+	if(f != stdin)
 		fclose(f);
-	if(numlines!=500)
+	if(numlines != 500)
 		return -1;
-	printf("A:%u\nC:%u\nG:%u\nT:%u\n", (uint16_t)occs, (uint16_t)(occs>>16),
-		(uint16_t)(occs>>32), (uint16_t)(occs>>48));
+	for(unsigned i=0; i<strlen(alphabet); i++)
+		printf("%c: %u\n", alphabet[i], (uint16_t)(occs >> (16*i)));
 	return 0;
 }
-- 
2.20.1