v1.1.1

INSTALL

@@ -7,10 +7,12 @@ Contents
 
 1. Dependencies
 ===============
-pIRS requires the following libraries to compile:
+pIRS requires the following libraries(with *-devel packages) to compile:
 
     zlib (http://www.zlib.net/)
     Boost Libraries (http://www.boost.org/)
+    glibc-static
+    libstdc++-static
 
 pIRS requires the following tools to generate and analyse profiles:
 

NEWS

@@ -1,3 +1,10 @@
+version 1.11
+	Fix one bug which lead to terminate called after throwing an instance of 'std::out_of_range' while simulate indel-error on reads with "pirs simulate".
+
+version 1.10
+	Fix one bug which will result in overlapping variation region in program "pirs diploid".
+	Add option -e to simulate different substiution-error rate in program "pirs simulate".
+
 version 1.01
 	Add EAMSS filter from CASAVA v.1.8.0 .
 

README

@@ -79,10 +79,10 @@ Contents
       -o <string> output prefix (default=ref_sequence)
       -h          output help information and exit
 
-  3.2 pirs simualte
+  3.2 pirs simulate
     Simulate sequencing data of Illumina sequencing platform
 
-    Usage: pirs simualte [OPTIONS]
+    Usage: pirs simulate [OPTIONS]
       -i <string> input reference sequence (file.fa / file.fa.gz)
       -I <string> another input reference for diploid genome (generated by "pirs diploid", 
                   set only when simulating reads of diploid genome)
@@ -122,7 +122,7 @@ Contents
       e) simulate_seq.o, simulate_seq.e: records of the program running information.
   4.2 Simulation result of Illumina sequencing data for haploid genome.
     Example command line:
-    pirs simualte -i Human_ref.fa -m 170 -l 90 -x 5 -v 10 -o Human >simulate_170.o 2>simulate_170.e
+    pirs simulate -i Human_ref.fa -m 170 -l 90 -x 5 -v 10 -o Human >simulate_170.o 2>simulate_170.e
     Output files:
       a) Human_90_170_1.fq.gz, Human_90_170_2.fq.gz: the pair-end read files.
       b) Human_90_170.error_rate.distr: the error distribution file.
@@ -131,7 +131,7 @@ Contents
       e) simulate_170.o, simulate_170.e: record the running information of program.
   4.3 Simulation result of Illumina sequencing data for diploid genome.
     Example command line:
-    pirs simualte -i Human_ref.fa -I Human.snp.indel.invertion.fa.gz -m 800 -l 70 -x 5 -v 10 
+    pirs simulate -i Human_ref.fa -I Human.snp.indel.invertion.fa.gz -m 800 -l 70 -x 5 -v 10 
                             -o Human >simulate_800.o 2>simulate_800.e
     Output files:
       a) Human_70_800_1.fq.gz, Human_70_800_2.fq.gz: the pair-end read files.
@@ -240,3 +240,4 @@ Contents
   of output data in file *.error_rate.distr .
 
   For update & support, please refer to http://code.google.com/p/pirs/ .
+