From 7a406388fad470fb5fc443b546523a4d87d96439 Mon Sep 17 00:00:00 2001
From: Mart Lubbers <mart@martlubbers.net>
Date: Mon, 2 Feb 2015 10:08:23 +0100
Subject: [PATCH] ass1 done

---
 ass1/mart/s4109503-s4202015-sws1.tar.gz       | Bin 0 -> 1237 bytes
 .../exercise2/parsegenome.c                   |  43 +++++++-----------
 2 files changed, 17 insertions(+), 26 deletions(-)
 create mode 100644 ass1/mart/s4109503-s4202015-sws1.tar.gz

diff --git a/ass1/mart/s4109503-s4202015-sws1.tar.gz b/ass1/mart/s4109503-s4202015-sws1.tar.gz
new file mode 100644
index 0000000000000000000000000000000000000000..d3162b4ba581c443375991e4bc6af69398d2a5dd
GIT binary patch
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diff --git a/ass1/mart/sws1-s4109503-s4202015/exercise2/parsegenome.c b/ass1/mart/sws1-s4109503-s4202015/exercise2/parsegenome.c
index eee156f..3faf91c 100644
--- a/ass1/mart/sws1-s4109503-s4202015/exercise2/parsegenome.c
+++ b/ass1/mart/sws1-s4109503-s4202015/exercise2/parsegenome.c
@@ -1,49 +1,40 @@
 #include <stdio.h>
 #include <stdlib.h>
+#include <string.h>
 
 int main(int argc, char* argv[])
 {
-	if(argc != 2)
-	{
-		printf("Usage: %s filepath\n", argv[0]);
-		return 2;
-	}
-
 	char c;
-	int charsperline = 0;
-	int numlines = 0;
-	int occs[4] = {0, 0, 0, 0};
-
-	FILE *f = fopen(argv[1], "r");
+	char charsperline = 0;
+	short numlines = 0;
+	long long unsigned int occs = 0;
+	/* When the filepath is not given or "-" assume stdin */
+	FILE *f = (argc!=2 || strcmp(argv[1], "-")==0) ? stdin : fopen(argv[1], "r");
 	if(f == NULL)
 	{
-		printf("Unable to open file...");
+		printf("Unable to open file or stdin...\n");
 		return 2;
 	}
-
 	while((c = fgetc(f)) != EOF)
 	{
-		if(c == '\n')
+		if(c == '\n' && charsperline == 100 && numlines <= 500)
 		{
-			if(charsperline != 100 || numlines > 500)
-				return -1;
 			numlines += 1;
 			charsperline = 0;
 		}
-		else
-		{
-/* Fancy polynome that translates A: 0, C: 1, G: 2, T: 3 */
-			if(c == 'A' || c == 'C' || c == 'G' || c == 'T')
-				occs[(int)(.001657140781*c*c*c-0.3780662484*c*c+28.74757194*c-726.3545635)] += 1;
-			else
-				return -1;
+		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
+			break;
 	}
-	fclose(f);
+	if(f != stdout)
+		fclose(f);
 	if(numlines != 500)
 		return -1;
-
-	printf("A: %d\nC: %d\nG: %d\nT: %d\n", occs[0], occs[1], occs[2], occs[3]);
+	printf("A: %llu\nC: %llu\nG: %llu\nT: %llu\n", occs & 0xFFFF,
+		(occs >> 16) & 0xFFFF, (occs >> 32) & 0xFFFF, (occs >> 48) & 0xFFFF);
 	return 0;
 }
-- 
2.20.1