Merge pull request #11 from acgtun/master

acgtun · acgtun · commit d91ce7cb3944 · 2015-07-15T17:09:16.000-07:00
update copyrights and format
diff --git a/Makefile b/Makefile
@@ -3,7 +3,7 @@
 #    Copyright (C) 2015 University of Southern California
 #                       Andrew D. Smith and Ting Chen
 #
-#    Authors: Andrew D. Smith, Ting Chen
+#    Authors: Haifeng Chen, Andrew D. Smith and Ting Chen
 #
 #    This program is free software: you can redistribute it and/or modify
 #    it under the terms of the GNU General Public License as published by
diff --git a/README.md b/README.md
@@ -77,7 +77,7 @@ For example, to mapping reads to human genome hg19
 
 	walt -i hg19.dbindex -r read_1.fq -o reads_1_mapping.sam
     
-If mapping the reads from the *_2 reads file, the -A option should be set. This means that all Gs in the reads and genome are transfered to As. If -A option is not set, all Cs in the reads and genome are transfered to Ts.
+If mapping the reads from the *_2 reads file, the -A option should be set. This means that all Gs in the reads and genome are converted to As. If -A option is not set, all Cs in the reads and genome are converted to Ts.
 
     walt -i hg19.dbindex -r read_2.fq -A -o reads_2_mapping.sam
     
diff --git a/src/Makefile b/src/Makefile
@@ -3,7 +3,7 @@
 #    Copyright (C) 2015 University of Southern California
 #                       Andrew D. Smith and Ting Chen
 #
-#    Authors: Andrew D. Smith, Ting Chen
+#    Authors: Haifeng Chen, Andrew D. Smith and Ting Chen
 #
 #    This program is free software: you can redistribute it and/or modify
 #    it under the terms of the GNU General Public License as published by
diff --git a/src/walt/Makefile b/src/walt/Makefile
@@ -3,7 +3,7 @@
 #    Copyright (C) 2015 University of Southern California
 #                       Andrew D. Smith and Ting Chen
 #
-#    Authors: Andrew D. Smith, Ting Chen
+#    Authors: Haifeng Chen, Andrew D. Smith and Ting Chen
 #
 #    This program is free software: you can redistribute it and/or modify
 #    it under the terms of the GNU General Public License as published by
diff --git a/src/walt/makedb.cpp b/src/walt/makedb.cpp
@@ -1,10 +1,10 @@
 /*
- *    This file is part of the WALT program
+ *    This is the main function to build index for reference genome.
  *
- *    Copyright (C) 2015 University of Southern California and
+ *    Copyright (C) 2015 University of Southern California
  *                       Andrew D. Smith and Ting Chen
  *
- *    Authors: Andrew D. Smith and Ting Chen
+ *    Authors: Haifeng Chen, Andrew D. Smith and Ting Chen
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
@@ -20,10 +20,6 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-/*
- * This is the main function to build index for reference genome.
- */
-
 #include <set>
 #include <string>
 #include <vector>
diff --git a/src/walt/mapping.cpp b/src/walt/mapping.cpp
@@ -1,10 +1,11 @@
 /*
- *    This file is part of the WALT program
+ *    This file contains the functions for mapping single-end reads.
+ *    The detail description of each function please refer to head file.
  *
- *    Copyright (C) 2015 University of Southern California and
+ *    Copyright (C) 2015 University of Southern California
  *                       Andrew D. Smith and Ting Chen
  *
- *    Authors: Andrew D. Smith and Ting Chen
+ *    Authors: Haifeng Chen, Andrew D. Smith and Ting Chen
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
diff --git a/src/walt/mapping.hpp b/src/walt/mapping.hpp
@@ -1,10 +1,10 @@
 /*
- *    This file is part of the WALT program
+ *    The head file for mapping single-end reads
  *
- *    Copyright (C) 2015 University of Southern California and
+ *    Copyright (C) 2015 University of Southern California
  *                       Andrew D. Smith and Ting Chen
  *
- *    Authors: Andrew D. Smith and Ting Chen
+ *    Authors: Haifeng Chen, Andrew D. Smith and Ting Chen
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
@@ -20,9 +20,6 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-/*
- * singled-end read mapping
- */
 #ifndef MAPPING_HPP_
 #define MAPPING_HPP_
 
@@ -107,10 +104,10 @@ string ReverseString(const string& str);
 /* reverse compliment string */
 string ReverseComplimentString(const string& str);
 
-/* reads from _1 file, Cs are transfered to Ts*/
+/* reads from _1 file, Cs are converted to Ts*/
 void C2T(const string& org_read, const uint32_t& read_len, string& read);
 
-/* reads from _2 file, Gs are transfered to As*/
+/* reads from _2 file, Gs are converted to As*/
 void G2A(const string& org_read, const uint32_t& read_len, string& read);
 
 /* find the region of index where those positions started with the seed */
diff --git a/src/walt/paired.cpp b/src/walt/paired.cpp
@@ -1,10 +1,11 @@
 /*
- *    This file is part of the WALT program
+ *    This file contains the functions for mapping paired-end reads.
+ *    The detail description of each function please refer to head file.
  *
- *    Copyright (C) 2015 University of Southern California and
+ *    Copyright (C) 2015 University of Southern California
  *                       Andrew D. Smith and Ting Chen
  *
- *    Authors: Andrew D. Smith and Ting Chen
+ *    Authors: Haifeng Chen, Andrew D. Smith and Ting Chen
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
diff --git a/src/walt/paired.hpp b/src/walt/paired.hpp
@@ -1,10 +1,10 @@
 /*
- *    This file is part of the WALT program
+ *    The head file for mapping paired-end reads
  *
- *    Copyright (C) 2015 University of Southern California and
+ *    Copyright (C) 2015 University of Southern California
  *                       Andrew D. Smith and Ting Chen
  *
- *    Authors: Andrew D. Smith and Ting Chen
+ *    Authors: Haifeng Chen, Andrew D. Smith and Ting Chen
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
@@ -20,10 +20,6 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-/*
- * paired-end read mapping
- */
-
 #ifndef PAIRED_HPP_
 #define PAIRED_HPP_
 
diff --git a/src/walt/reference.cpp b/src/walt/reference.cpp
@@ -1,10 +1,11 @@
 /*
- *    This file is part of the WALT program
+ *    The file contains the functions for building index.
+ *    The detail description of each function please refer to head file.
  *
- *    Copyright (C) 2015 University of Southern California and
+ *    Copyright (C) 2015 University of Southern California
  *                       Andrew D. Smith and Ting Chen
  *
- *    Authors: Andrew D. Smith and Ting Chen
+ *    Authors: Haifeng Chen, Andrew D. Smith and Ting Chen
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
diff --git a/src/walt/reference.hpp b/src/walt/reference.hpp
@@ -1,10 +1,10 @@
 /*
- *    This file is part of the WALT program
+ *    The is the header file for building index.
  *
- *    Copyright (C) 2015 University of Southern California and
+ *    Copyright (C) 2015 University of Southern California
  *                       Andrew D. Smith and Ting Chen
  *
- *    Authors: Andrew D. Smith and Ting Chen
+ *    Authors: Haifeng Chen, Andrew D. Smith and Ting Chen
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
@@ -24,10 +24,10 @@
  * reference.cpp loads chromosomes from the genome file, builds hash table
  * and stores them in struct Genome and HashTable.
  *
- * All the characters in the genome are transfered into capital letters.
+ * All the characters in the genome are converted into capital letters.
  *
- * Ns in the genome are transfered to T when mapping _1 read files, and
- * transfered to G when mapping _2 read files.
+ * Ns in the genome are converted to T when mapping _1 read files, and
+ * converted to A when mapping _2 read files.
  */
 
 #ifndef REFERENCE_H_
@@ -108,10 +108,10 @@ void ReadGenome(const vector<string>& chrom_files, Genome& genome);
 /* get the reverse complimentary strand of genome */
 void ReverseGenome(Genome& genome);
 
-/* Cs in the genome are transferred to Ts */
+/* Cs in the genome are converted to Ts */
 void C2T(vector<char>& sequence);
 
-/* Gs in the genome are transferred to As */
+/* Gs in the genome are converted to As */
 void G2A(vector<char>& sequence);
 
 /* count how many k-mers for each hash value (bucket) */
diff --git a/src/walt/util.hpp b/src/walt/util.hpp
@@ -1,10 +1,10 @@
 /*
  *    This file is part of the WALT program
  *
- *    Copyright (C) 2015 University of Southern California and
+ *    Copyright (C) 2015 University of Southern California
  *                       Andrew D. Smith and Ting Chen
  *
- *    Authors: Andrew D. Smith and Ting Chen
+ *    Authors: Authors: Haifeng Chen, Andrew D. Smith and Ting Chen
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
@@ -37,7 +37,7 @@
 #include <limits>
 #include <string>
 
-const char walt_version[] = "0.4";
+const char walt_version[] = "1.0";
 
 //#define SEEDPATTERN7
 #ifdef SEEDPATTERN7
diff --git a/src/walt/walt.cpp b/src/walt/walt.cpp
@@ -1,10 +1,10 @@
 /*
- *    This file is part of the WALT program
+ *    This is the main function for bisulfite sequencing mapping.
  *
- *    Copyright (C) 2015 University of Southern California and
+ *    Copyright (C) 2015 University of Southern California
  *                       Andrew D. Smith and Ting Chen
  *
- *    Authors: Andrew D. Smith and Ting Chen
+ *    Authors: Haifeng Chen, Andrew D. Smith and Ting Chen
  *
  *    This program is free software: you can redistribute it and/or modify
  *    it under the terms of the GNU General Public License as published by
@@ -20,10 +20,6 @@
  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
  */
 
-/*
- * This is the main function for bisulfite sequencing mapping.
- */
-
 #include <vector>
 #include <string>
 
@@ -82,9 +78,9 @@ int main(int argc, const char **argv) {
     bool unmapped = false;
 
     /* AG_WILDCARD is false by default, which means that all Cs
-     * in the reads and genome are transfered to Ts.
+     * in the reads and genome are converted to Ts.
      * If AG_WILDCARD is true, all Gs in the reads and genome
-     * are transfered to As. If option is only for single-end mapping */
+     * are converted to As. If option is only for single-end mapping */
     bool AG_WILDCARD = false;
 
     /* maximum allowed mismatches */

Original file line number	Diff line number	Diff line change
`@@ -3,7 +3,7 @@`
`3`	`3`	`# Copyright (C) 2015 University of Southern California`
`4`	`4`	`# Andrew D. Smith and Ting Chen`
`5`	`5`	`#`
`6`		`-# Authors: Andrew D. Smith, Ting Chen`
	`6`	`+# Authors: Haifeng Chen, Andrew D. Smith and Ting Chen`
`7`	`7`	`#`
`8`	`8`	`# This program is free software: you can redistribute it and/or modify`
`9`	`9`	`# it under the terms of the GNU General Public License as published by`
Original file line number	Diff line number	Diff line change
`@@ -1,10 +1,11 @@`
`1`	`1`	`/*`
`2`		`- * This file is part of the WALT program`
	`2`	`+ * This file contains the functions for mapping single-end reads.`
	`3`	`+ * The detail description of each function please refer to head file.`
`3`	`4`	`*`
`4`		`- * Copyright (C) 2015 University of Southern California and`
	`5`	`+ * Copyright (C) 2015 University of Southern California`
`5`	`6`	`* Andrew D. Smith and Ting Chen`
`6`	`7`	`*`
`7`		`- * Authors: Andrew D. Smith and Ting Chen`
	`8`	`+ * Authors: Haifeng Chen, Andrew D. Smith and Ting Chen`
`8`	`9`	`*`
`9`	`10`	`* This program is free software: you can redistribute it and/or modify`
`10`	`11`	`* it under the terms of the GNU General Public License as published by`