From 5715c423ff52c91e013fc5524f64e48927a2fa11 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Sun, 17 Sep 2017 15:21:36 -0400
Subject: [PATCH] exposed timer and verbose-level to mappy

---
 python/cmappy.h   | 12 ++++++++++++
 python/cmappy.pxd |  4 ++++
 python/mappy.pyx  |  8 +++++++-
 3 files changed, 23 insertions(+), 1 deletion(-)

diff --git a/python/cmappy.h b/python/cmappy.h
index 127fc68..c696a80 100644
--- a/python/cmappy.h
+++ b/python/cmappy.h
@@ -55,4 +55,16 @@ static inline void mm_fastx_close(kseq_t *ks)
 	gzclose(fp);
 }
 
+static inline int mm_verbose_level(int v)
+{
+	if (v >= 0) mm_verbose = v;
+	return mm_verbose;
+}
+
+static inline void mm_reset_timer(void)
+{
+	extern double realtime(void);
+	mm_realtime0 = realtime();
+}
+
 #endif
diff --git a/python/cmappy.pxd b/python/cmappy.pxd
index b4f821d..5e797ef 100644
--- a/python/cmappy.pxd
+++ b/python/cmappy.pxd
@@ -32,6 +32,7 @@ cdef extern from "minimap.h":
 		int mini_batch_size
 
 	int mm_set_opt(char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
+	int mm_verbose
 
 	#
 	# Indexing
@@ -106,3 +107,6 @@ cdef extern from "cmappy.h":
 	kseq_t *mm_fastx_open(const char *fn)
 	void mm_fastx_close(kseq_t *ks)
 	int kseq_read(kseq_t *seq)
+
+	int mm_verbose_level(int v)
+	void mm_reset_timer()
diff --git a/python/mappy.pyx b/python/mappy.pyx
index 0b56673..649526e 100644
--- a/python/mappy.pyx
+++ b/python/mappy.pyx
@@ -2,6 +2,8 @@ from libc.stdint cimport uint8_t, int8_t
 from libc.stdlib cimport free
 cimport cmappy
 
+cmappy.mm_reset_timer()
+
 cdef class Alignment:
 	cdef int _ctg_len, _r_st, _r_en
 	cdef int _q_st, _q_en
@@ -139,7 +141,11 @@ def fastx_read(fn):
 	ks = cmappy.mm_fastx_open(str.encode(fn))
 	if ks is NULL: return None
 	while cmappy.kseq_read(ks) >= 0:
-		qual = None
 		if ks.qual.l > 0: qual = str(ks.qual.s)
+		else qual = None
 		yield str(ks.name.s), str(ks.seq.s), qual
 	cmappy.mm_fastx_close(ks)
+
+def verbose(v=None):
+	if v is None: v = -1
+	return cmappy.mm_verbose_level(v)