From 79bcbb4514bc013d87f1a03ca80d8c781c3a6dad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ren=C3=A9=20Warren?= Date: Sun, 22 Nov 2020 11:36:41 -0800 Subject: [PATCH] ntedit v1.3.3 support for IUPAC nucleotide codes --- README.md | 4 ++-- ntedit.cpp | 24 +++++++++++++++++------- 2 files changed, 19 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 013fa63..1664b96 100755 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ [![Release](https://img.shields.io/github/release/bcgsc/ntEdit.svg)](https://github.com/bcgsc/ntEdit/releases) -[![Downloads](https://img.shields.io/github/downloads/bcgsc/ntEdit/total?logo=github)](https://github.com/bcgsc/ntEdit/releases/download/v1.3.2/ntEdit_v1-3-2.tar.gz) +[![Downloads](https://img.shields.io/github/downloads/bcgsc/ntEdit/total?logo=github)](https://github.com/bcgsc/ntEdit/releases/download/v1.3.3/ntEdit_v1-3-3.tar.gz) [![Conda](https://img.shields.io/conda/dn/bioconda/ntedit?label=Conda)](https://anaconda.org/bioconda/ntedit) [![Issues](https://img.shields.io/github/issues/bcgsc/ntEdit.svg)](https://github.com/bcgsc/ntEdit/issues) Thank you for your [![Stars](https://img.shields.io/github/stars/bcgsc/ntEdit.svg)](https://github.com/bcgsc/ntEdit/stargazers) @@ -161,7 +161,7 @@ eg. 
 e.g. ./ntedit -f ecoliWithMismatches001Indels0001.fa -r solidBF_k25.bf -b ntEditEcolik25
 
-ntEdit v1.3.2
+ntEdit v1.3.3
 
 Scalable genome sequence polishing.
 
diff --git a/ntedit.cpp b/ntedit.cpp
index 1fef9d6..2bdd073 100644
--- a/ntedit.cpp
+++ b/ntedit.cpp
@@ -30,15 +30,15 @@ KSEQ_INIT(gzFile, gzread)
 
 // NOLINTNEXTLINE(modernize-avoid-c-arrays)
 static const char VERSION_MESSAGE[] =
-    PROGRAM " version 1.3.2\n"
+    PROGRAM " version 1.3.3\n"
             "written by Rene Warren, Hamid Mohamadi, and Jessica Zhang.\n"
             "copyright 2018-2020 Canada's Michael smith Genome Science Centre\n";
 
 // NOLINTNEXTLINE(modernize-avoid-c-arrays)
 static const char USAGE_MESSAGE[] = PROGRAM
-    " v1.3.2\n"
+    " v1.3.3\n"
     "\n"
-    "Scalable genome sequence polishing.\n"
+    "Fast, lightweight, scalable genome sequence polishing & snv detection*\n"
     "\n"
     " Options:\n"
     "	-t,	number of threads [default=1]\n"
@@ -149,6 +149,16 @@ std::unordered_map> bases_array = {
 	{ 'T', { 'A', 'C', 'G' } },
 	{ 'C', { 'A', 'T', 'G' } },
 	{ 'G', { 'A', 'T', 'C' } },
+	{ 'R', { 'T', 'C' } },
+	{ 'Y', { 'A', 'G' } },
+	{ 'S', { 'A', 'T' } },
+	{ 'W', { 'C', 'G' } },
+	{ 'K', { 'A', 'C' } },
+	{ 'M', { 'T', 'G' } },
+	{ 'B', { 'A' } },
+	{ 'D', { 'C' } },
+	{ 'H', { 'G' } },
+	{ 'V', { 'T' } },
 	{ 'N', { 'A', 'T', 'C', 'G' } }
 };
 
@@ -315,7 +325,7 @@ assert_readable(const std::string& path)
 bool
 isAcceptedBase(unsigned char C)
 {
-	return (C == 'A' || C == 'T' || C == 'G' || C == 'C');
+	return (C == 'A' || C == 'T' || C == 'G' || C == 'C' || C == 'R' || C == 'Y' || C == 'S' || C == 'W' || C == 'K' || C == 'M' || C == 'B' || C == 'D' || C == 'H' || C == 'V');
 }
 
 char
@@ -1747,7 +1757,7 @@ readAndCorrect(BloomFilter& bloom, BloomFilter& bloomrep)
 	}
 
 	vfout << "##fileDate=" << year << month << day << std::endl;
-	vfout << "##source=ntEditV1.3.2" << std::endl;
+	vfout << "##source=ntEditV1.3.3" << std::endl;
 	vfout << "##reference=file:" << opt::draft_filename << std::endl;
 	vfout << "##INFO=" << std::endl;
 	vfout << "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tINTEGRATION" << std::endl;
@@ -2030,11 +2040,11 @@ main(int argc, char** argv)
 		// print bloom filter details
 		bloomrep.printBloomFilterDetails();
 
-		std::cout << "\n---------- reading and polishing draft              : " << ctime(&rawtime);
+		std::cout << "\n---------- reading/processing input sequence        : " << ctime(&rawtime);
 		readAndCorrect(bloom, bloomrep);
 
 	} else {
-		std::cout << "---------- reading and polishing draft              : " << ctime(&rawtime);
+		std::cout << "---------- reading/processing input sequence        : " << ctime(&rawtime);
 		BloomFilter bloomrep(1000, 1, 1);
 		readAndCorrect(bloom, bloomrep);
 	}