Decrease memory footprint during alignment

BenLangmead · Jul 4, 2020 · cc62789 · cc62789
1 parent 01182df
commit cc62789
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Showing 3 changed files with 7 additions and 5 deletions.
diff --git a/pat.h b/pat.h
@@ -93,6 +93,8 @@ struct PerThreadReadBuf {
 
 	PerThreadReadBuf(size_t max_buf) :
 		max_buf_(max_buf),
+		bufa_(max_buf),
+		bufb_(max_buf),
 		rdid_()
 	{
 		bufa_.resize(max_buf);

diff --git a/read.h b/read.h
@@ -41,7 +41,7 @@ struct HitSet;
  */
 struct Read {
 
-	typedef SStringExpandable<char, 1024, 2, 1024> TBuf;
+	typedef SStringExpandable<char, 0, 2, 2048> TBuf;
 
 	Read() { reset(); }
 

diff --git a/sstring.h b/sstring.h
@@ -3492,9 +3492,9 @@ class SDnaMaskString : public SStringExpandable<char, S, M> {
 	virtual const char* toZBuf() const { return this->toZBufXForm(iupacs); }
 };
 
-typedef SStringExpandable<char, 1024, 2> BTString;
-typedef SDnaStringExpandable<1024, 2>    BTDnaString;
-typedef SDnaMaskString<32, 2>            BTDnaMask;
-typedef SString<char>                    BTRefString;
+typedef SStringExpandable<char, 25, 2>	BTString;
+typedef SDnaStringExpandable<25, 2>	BTDnaString;
+typedef SDnaMaskString<32, 2>           BTDnaMask;
+typedef SString<char>                   BTRefString;
 
 #endif /* SSTRING_H_ */