Updated version number in configure.ac and updated reference

README.md

@@ -1,10 +1,10 @@
 
-# MAPseq v1.2 (23 Oct 2017)
+# MAPseq v1.2.2 (30 Oct 2017)
 by Joao F. Matias Rodrigues, Thomas S.B. Schmidt, Janko Tackmann, and Christian von Mering  
 Institute of Molecular Life Sciences, University of Zurich, Switzerland
 
 Reference:
-Matias Rodrigues JF, Schmidt TSB, Tackmann J, Mering C von. MAPseq: bringing speed, accuracy and consistency to metagenomic ribosomal RNA analysis. submitted.
+Matias Rodrigues JF, Schmidt TSB, Tackmann J & von Mering C (2017) MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis. Bioinformatics. http://doi.org/10.1093/bioinformatics/btx517
 
 ---
 ## Table of contents
@@ -142,6 +142,9 @@ query1	FJ560320:1..876	301	0.7369985	301	0	0	0	301	305	606	+		Archaea		Archaea;F
 
 
 ## 4. HISTORY
+1.2.2 (30 Oct 2017)
+- Fixed multithreaded race condition causing issues on some systems.
+
 1.2.1 (23 Oct 2017)
 - Updated mapref to v2.2. Fixed several issues with v2.0.
 - Dropped LTP taxonomy due to low coverage.
@@ -156,4 +159,3 @@ query1	FJ560320:1..876	301	0.7369985	301	0	0	0	301	305	606	+		Archaea		Archaea;F
 1.0 (14 October 2016)  
 - First release of MAPseq.  
 
-

configure.ac

@@ -1,4 +1,4 @@
-AC_INIT([mapseq],[1.2.1])
+AC_INIT([mapseq],[1.2.2])
 
 : ${CXXFLAGS=-O3}
 

make-bin-package.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-./configure --prefix=`pwd`/mapseq-1.2-linux --bindir=`pwd`/mapseq-1.2-linux --enable-makestatic LIBS="-lgpm -ltermcap" CXXFLAGS="-O2"
+./configure --prefix=`pwd`/mapseq-1.2.2-linux --bindir=`pwd`/mapseq-1.2.2-linux --enable-makestatic LIBS="-lgpm -ltermcap" CXXFLAGS="-O2"
 #make install
 #cp README mapseq-1.0-bin/
 #rm -rf mapseq-1.0-bin/{esh,eutils-config,include,lib} 

man/mapseq.1

@@ -1,5 +1,5 @@
 .\" Process this file with
-.\" groff -man -Tascii hpc-clust.1
+.\" groff -man -Tascii mapseq.1
 .\"
 .TH MAPSEQ 1.2.1 "OCT 2017" Linux "User Manuals"
 .SH NAME

mapseq.cpp

@@ -110,6 +110,7 @@ class esearchws
 {
  public:
 //  eintarray best;
+  ernd rng;
   ealignws alignws;
   eintarray otukmerpos;
   uint64_t *kmerbitmask;
@@ -2983,10 +2984,10 @@ void otukmeradd(ebasicarray<deque<int> >& otukmers,int i,eseq& s,eintarray& tmpk
   }
 }
 
-void randomize(eintarray& seqids)
+void randomize(ernd& prnd,eintarray& seqids)
 {
   for (int i=seqids.size()-1; i>0; --i){
-    int r=int(rnd.uniform()*(i+1));
+    int r=int(prnd.uniform()*(i+1));
     if (r!=i) seqids.swap(r,i);
   }
 }
@@ -3232,7 +3233,7 @@ void seqsearch(const estr& str2id,eseqdb& db,eseq& s,earray<epredinfo>& pinfoarr
 
 //    cout << "# 2nd counting" << endl;
 
-    randomize(seqids);
+    randomize(sws.rng,seqids);
     sws.idcount.init(seqids.size(),0);
 
     if (sws.maskid+1u<sws.maskid){