From 9305e6aff665d3af46a6f170cdb2aefc60983395 Mon Sep 17 00:00:00 2001
From: cypridina <darrin.schultz91@gmail.com>
Date: Tue, 17 Oct 2017 23:15:44 -0700
Subject: [PATCH 1/2] arithemetic mean of qual rather than geometric

---
 addon.c | 12 ++++++++++++
 addon.h |  2 ++
 lex.c   |  1 +
 3 files changed, 15 insertions(+)

diff --git a/addon.c b/addon.c
index 7f6d6c3..bae4879 100644
--- a/addon.c
+++ b/addon.c
@@ -230,6 +230,18 @@ Cell *bio_func(int f, Cell *x, Node **a)
 				if (buf[i] - 33 >= thres) ++cnt;
 			setfval(y, (Awkfloat)cnt);
 		}
+	} else if (f == BIO_FARITHMEANQUAL) {
+		char *buf;
+		int i, l = 0;
+        double total_qual = 0.0;
+		buf = getsval(x);
+        /*printf("%s \n", buf);*/
+		l = strlen(buf);
+		if (l) { /* don't try for empty strings */
+			for (i = 0; i < l; ++i)
+				total_qual += pow(10, -((double)(buf[i] - 33) / 10) );
+			setfval(y, (Awkfloat)(-10 * log10(total_qual / l)) );
+		}
 	} /* else: never happens */
 	return y;
 }
diff --git a/addon.h b/addon.h
index e86552e..e5b96f6 100644
--- a/addon.h
+++ b/addon.h
@@ -41,6 +41,8 @@ int bio_getrec(char **pbuf, int *psize, int isrecord);
 #define BIO_FMEANQUAL 204
 #define BIO_FQUALCOUNT 205
 #define BIO_FTRIMQ    206
+#define BIO_FARITHMEANQUAL 207
+
 
 
 struct Cell;
diff --git a/lex.c b/lex.c
index d470364..a3cf5d3 100644
--- a/lex.c
+++ b/lex.c
@@ -48,6 +48,7 @@ Keyword keywords[] ={	/* keep sorted: binary searched */
 	{ "END",	XEND,		XEND },
 	{ "NF",		VARNF,		VARNF },
 	{ "and",	BIO_FAND,	BLTIN },
+	{ "arithmeanqual",	BIO_FARITHMEANQUAL,		BLTIN },
 	{ "atan2",	FATAN,		BLTIN },
 	{ "break",	BREAK,		BREAK },
 	{ "close",	CLOSE,		CLOSE },

From 8cfe170b9fb5340f25a725fcb49ca22489f13ffa Mon Sep 17 00:00:00 2001
From: cypridina <darrin.schultz91@gmail.com>
Date: Tue, 17 Oct 2017 23:18:50 -0700
Subject: [PATCH 2/2] spaces to tabs, commented

---
 addon.c | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/addon.c b/addon.c
index bae4879..d8e58ed 100644
--- a/addon.c
+++ b/addon.c
@@ -233,14 +233,14 @@ Cell *bio_func(int f, Cell *x, Node **a)
 	} else if (f == BIO_FARITHMEANQUAL) {
 		char *buf;
 		int i, l = 0;
-        double total_qual = 0.0;
+		double total_qual = 0.0;
 		buf = getsval(x);
-        /*printf("%s \n", buf);*/
 		l = strlen(buf);
 		if (l) { /* don't try for empty strings */
-			for (i = 0; i < l; ++i)
+			for (i = 0; i < l; ++i) /*convert Q-score to e-rate*/
 				total_qual += pow(10, -((double)(buf[i] - 33) / 10) );
-			setfval(y, (Awkfloat)(-10 * log10(total_qual / l)) );
+			/* mean of e-rate -> Q-score */
+			setfval(y, (Awkfloat)(-10 * log10(total_qual / l)) ); 
 		}
 	} /* else: never happens */
 	return y;