New upstream version 1.92.3 (66923111) · Commits · Debian Med / htqc

CMakeLists.txt

+1 −1

Original line number	Diff line number	Diff line
		@@ -27,7 +27,7 @@ list(APPEND CMAKE_CXX_FLAGS "-std=c++11")

		set(CPACK_PACKAGE_VERSION_MAJOR 1)
		set(CPACK_PACKAGE_VERSION_MINOR 92)
		set(CPACK_PACKAGE_VERSION_PATCH 1)
		set(CPACK_PACKAGE_VERSION_PATCH 3)
		set(CPACK_GENERATOR TGZ)
		set(CPACK_SOURCE_GENERATOR TGZ)
		set(CPACK_SOURCE_IGNORE_FILES ${CPACK_SOURCE_IGNORE_FILES} ".kdev4" "~" "build" "nbproject" "test_data" "CMakeLists.txt.user*")

Changes.md

+18 −0

Original line number	Diff line number	Diff line
		Changes
		=======

		1.92.3
		======

		- htio2 library

		Fixed bugs on missing move constructor of Option class, and now it works
		properly with GCC 4.7.

		1.92.2
		======

		- Refined unit test for ht2-overlap.

		- htio2 library

		Fixed a bug on command-line option parser, where values with leading "-"
		was recognized as option key.

		1.92.1
		======

src/htio2/OptionParser.cpp

+49 −24

Original line number	Diff line number	Diff line
		@@ -101,8 +101,21 @@ string Option::BoolSwitch::to_string()
		return "";
		}

		Option::Option(Option &&other) noexcept
		: name_long(other.name_long)
		, name_short(other.name_short)
		, group(other.group)
		, store(other.store)
		, flags(other.flags)
		, option_desc(other.option_desc)
		, value_desc(other.value_desc)
		{
		other.store = nullptr;
		}

		Option::~Option()
		{
		if (store)
		delete store;
		}

		@@ -262,22 +275,31 @@ void OptionParser::parse_options(int& argc, char** argv)
		{
		// long key in "--xxx" style
		if (curr_token[1] == '-')
		{
		Option* next_option = find_option_long(curr_token);

		if (next_option)
		{
		// clear previous values
		_dump_value_group_(values_by_option, curr_option, curr_value_group);

		// find option object
		curr_option = find_option_long(curr_token);
		curr_option = next_option;
		}
		else
		{
		curr_value_group.emplace_back(i, curr_token);
		}
		}

		// short key in "-x" style
		else
		{
		Option* next_option = find_option_short(curr_token[1]);

		if (next_option)
		{
		// clear previous values
		_dump_value_group_(values_by_option, curr_option, curr_value_group);

		// find option object
		curr_option = find_option_short(curr_token[1]);
		curr_option = next_option;

		// short key contains a value
		if (curr_token.length() > 2)
		@@ -292,7 +314,12 @@ void OptionParser::parse_options(int& argc, char** argv)
		exit(EXIT_FAILURE);
		}

		curr_value_group.push_back(make_pair(i, curr_token_value));
		curr_value_group.emplace_back(i, curr_token_value);
		}
		}
		else
		{
		curr_value_group.emplace_back(i, curr_token);
		}
		}
		}
		@@ -515,8 +542,7 @@ Option* OptionParser::find_option_long(const string &key)

		if (matched_keys.size() == 0)
		{
		fprintf(stderr, "ERROR: unknown option \"%s\"\n", key.c_str());
		exit(EXIT_FAILURE);
		return nullptr;
		}
		else if (matched_keys.size() == 1)
		{
		@@ -538,8 +564,7 @@ Option* OptionParser::find_option_short(char key)
		return options[it->second];
		else
		{
		fprintf(stderr, "ERROR: unknown option \"-%c\"\n", key);
		exit(EXIT_FAILURE);
		return nullptr;
		}
		}

src/htio2/OptionParser.h

+6 −4

Original line number	Diff line number	Diff line
		@@ -180,11 +180,13 @@ public:
		{
		}

		virtual ~Option();
		Option(Option&& other) noexcept;

		// copying is not allowed
		Option(const Option& other) = delete;
		Option& operator = (const Option& other) = delete;

		private:
		Option(const Option& other);
		Option& operator = (const Option& other);
		virtual ~Option();

		protected:
		static bool validate_name(char name);

t/t_ht_overlap.cpp

+118 −3

Original line number	Diff line number	Diff line
		#include "TestFramework.h"
		#include "TestConfig.h"

		#include "htio2/FastqIO.h"
		#include "htio2/PairedEndIO.h"
		#include "htio2/FastqSeq.h"

		#include <map>

		using namespace std;
		using namespace htio2;
		using namespace htio2::juce;

		void parse_fields(const string& desc, map<string, int>& result)
		{
		StringArray tokens;
		tokens.addTokens(String(desc), " =", "");
		if (tokens.size() % 2)
		{
		fprintf(stderr, "invalid token size %d, not even\n", tokens.size());
		abort();
		}
		for (int i = 0; i < tokens.size(); i+=2)
		{
		const String& key = tokens[i];
		const String& value = tokens[i+1];
		result[key.toStdString()] = value.getIntValue();
		}
		}

		void TestFramework::content()
		{
		const char* cmd = "../src/ht2-overlap -q -i " TEST_SOURCE_DIR "/test1.fastq.gz " TEST_SOURCE_DIR "/test2.fastq.gz -o ovlp -u novlp";
		ok(!system(cmd), cmd);
		OK(text_file_eq("ovlp.fastq.gz", TEST_SOURCE_DIR "/test_ovlp.fastq.gz"));
		OK(text_file_eq("novlp_1.fastq.gz", TEST_SOURCE_DIR "/test_novlp_1.fastq.gz"));
		OK(text_file_eq("novlp_2.fastq.gz", TEST_SOURCE_DIR "/test_novlp_2.fastq.gz"));


		map<string,string> ovlp_seqs;
		map<string,int> offsets;
		{
		htio2::FastqIO fh_ovlp("ovlp.fastq.gz", htio2::READ);
		htio2::FastqSeq seq;
		while (fh_ovlp.next_seq(seq))
		{
		map<string,int> attrs;
		parse_fields(seq.desc, attrs);
		if (!attrs.count("kmer_pos_a"))
		{
		fprintf(stderr, "no attribute kmer_pos_a\n");
		abort();
		}
		if (!attrs.count("kmer_pos_b"))
		{
		fprintf(stderr, "no attribute kmer_pos_b\n");
		abort();
		}

		ovlp_seqs[seq.id] = seq.seq;
		offsets[seq.id] = attrs["kmer_pos_b"] - attrs["kmer_pos_a"];
		}
		}

		{
		htio2::FastqSeq seq1;
		htio2::FastqSeq seq2;
		htio2::PairedEndIO fh_in(TEST_SOURCE_DIR "/test1.fastq.gz", TEST_SOURCE_DIR "/test2.fastq.gz",
		htio2::READ);
		while (fh_in.next_pair(seq1,seq2))
		{
		if (seq1.id != seq2.id)
		{
		fprintf(stderr, "conflict ID: %s and %s\n", seq1.id.c_str(), seq2.id.c_str());
		abort();
		}

		if (!ovlp_seqs.count(seq1.id))
		continue;

		const string& merged_seq = ovlp_seqs[seq1.id];
		int offset = offsets[seq1.id];

		for (int i = 0; i < merged_seq.length(); i++)
		{
		int i1 = numeric_limits<int>::max();
		int i2 = numeric_limits<int>::max();

		if (offset >= 0)
		{
		i1 = i - offset;
		i2 = i;
		}
		else
		{
		i1 = i;
		i2 = i + offset;
		}

		if (0 <= i1 && i1 < seq1.length())
		{
		if (0 <= i2 && i2 < seq2.length())
		{
		if (seq1.quality[i1] >= seq2.quality[i2])
		IS(seq1.seq[i1], merged_seq[i]);
		else
		IS(seq2.seq[i2], merged_seq[i]);
		}
		else
		{
		IS(seq1.seq[i1], merged_seq[i]);
		}
		}
		else
		{
		if (0 <= i2 && i2 < seq2.length())
		{
		IS(seq2.seq[i2], merged_seq[i]);
		}
		else
		{
		fprintf(stderr, "invalid position %d and %d at %d", i1, i2, i);
		abort();
		}
		}
		}
		}
		}
		}