From b30315f84a312370a69561dae09f89ce9bb3cd52 Mon Sep 17 00:00:00 2001
From: Mart Lubbers <mart@martlubbers.net>
Date: Tue, 3 Feb 2015 16:28:56 +0100
Subject: [PATCH] final ass1

---
 .../sws1-s4109503-s4202015/exercise1/commands |  2 +-
 .../sws1-s4109503-s4202015/exercise2/Makefile | 10 ++++-
 .../exercise2/parsegenome.c                   | 37 +++++++------------
 3 files changed, 22 insertions(+), 27 deletions(-)

diff --git a/ass1/mart/sws1-s4109503-s4202015/exercise1/commands b/ass1/mart/sws1-s4109503-s4202015/exercise1/commands
index ef8e2bc..8748d46 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}
 cd sws1-s4109503-s4202015
 echo -e "s4109503: Mart Lubbers\ns4202015: Chris Kamphuis" > names.txt
-du -cb | tail -1 | cut -f 1 > exercise1/1b.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 95d7d4d..e7ef6d1 100644
--- a/ass1/mart/sws1-s4109503-s4202015/exercise2/Makefile
+++ b/ass1/mart/sws1-s4109503-s4202015/exercise2/Makefile
@@ -1,2 +1,8 @@
-all:
-	gcc -Wall parsegenome.c -o parsegenome
+CC=gcc
+CFLAGS=-Wall -Wextra
+
+all: parsegenome.c
+	$(CC) $(CFLAGS) parsegenome.c -o parsegenome
+
+clean:
+	rm -vf parsegenome
diff --git a/ass1/mart/sws1-s4109503-s4202015/exercise2/parsegenome.c b/ass1/mart/sws1-s4109503-s4202015/exercise2/parsegenome.c
index 3faf91c..d561d4f 100644
--- a/ass1/mart/sws1-s4109503-s4202015/exercise2/parsegenome.c
+++ b/ass1/mart/sws1-s4109503-s4202015/exercise2/parsegenome.c
@@ -1,40 +1,29 @@
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
+#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            */
 int main(int argc, char* argv[])
 {
 	char c;
 	char charsperline = 0;
 	short numlines = 0;
-	long long unsigned int occs = 0;
-	/* When the filepath is not given or "-" assume stdin */
+	uint64_t occs = 0;
 	FILE *f = (argc!=2 || strcmp(argv[1], "-")==0) ? stdin : fopen(argv[1], "r");
 	if(f == NULL)
-	{
-		printf("Unable to open file or stdin...\n");
 		return 2;
-	}
-	while((c = fgetc(f)) != EOF)
-	{
-		if(c == '\n' && charsperline == 100 && numlines <= 500)
-		{
-			numlines += 1;
+	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)
-		{ /*Fancy polynomial that translates the ascii value to a bitshift*/
-			occs += 1LL<<(int)(0.026514*c*c*c-6.049*c*c+459.96*c-11621.2);
-			charsperline += 1;
-		}
+		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
 			break;
-	}
 	if(f != stdout)
 		fclose(f);
-	if(numlines != 500)
+	if(numlines!=500)
 		return -1;
-	printf("A: %llu\nC: %llu\nG: %llu\nT: %llu\n", occs & 0xFFFF,
-		(occs >> 16) & 0xFFFF, (occs >> 32) & 0xFFFF, (occs >> 48) & 0xFFFF);
+	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));
 	return 0;
 }
-- 
2.20.1