New upstream version 5.3.2 (a7a0425a) · Commits · Debian Med / blasr

.clang-format

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		BasedOnStyle: Google
		BreakBeforeBraces: Mozilla

		AllowShortLoopsOnASingleLine: false
		AccessModifierOffset: -4
		BreakConstructorInitializersBeforeComma: true
		ColumnLimit: 100
		IndentWidth: 4
		PointerAlignment: Left
		TabWidth: 4

		ReflowComments: false # protect ASCII art in comments
		KeepEmptyLinesAtTheStartOfBlocks: true

.gitignore

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		@@ -3,6 +3,7 @@ defines.mk
		*.o
		*.err
		blasr
		build/
		/utils/bam2bax/build/
		/utils/bam2bax/bin/
		/utils/bam2bax/tests/bin/
		@@ -11,3 +12,8 @@ blasr
		/utils/bax2bam/bin/
		/utils/bax2bam/tests/bin/
		/utils/bax2bam/tests/src/TestData.h

		# Meson WrapDB stuff
		subprojects/packagecache/
		subprojects/blasr_libcpp*
		subprojects/pbbam*

.gitmodules

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		[submodule "libcpp"]
		path = libcpp
		url = git://github.com/PacificBiosciences/blasr_libcpp.git

Blasr.cpp

+803 −873

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BlasrGitHash.h.in

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		// Copyright (c) 2016, Pacific Biosciences of California, Inc.
		//
		// All rights reserved.
		//
		// Redistribution and use in source and binary forms, with or without
		// modification, are permitted (subject to the limitations in the
		// disclaimer below) provided that the following conditions are met:
		//
		// * Redistributions of source code must retain the above copyright
		// notice, this list of conditions and the following disclaimer.
		//
		// * Redistributions in binary form must reproduce the above
		// copyright notice, this list of conditions and the following
		// disclaimer in the documentation and/or other materials provided
		// with the distribution.
		//
		// * Neither the name of Pacific Biosciences nor the names of its
		// contributors may be used to endorse or promote products derived
		// from this software without specific prior written permission.
		//
		// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
		// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
		// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
		// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
		// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
		// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
		// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
		// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
		// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
		// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
		// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
		// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
		// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
		// SUCH DAMAGE.

		// Author: Armin Töpfer

		#pragma once

		#include <string>

		namespace PacBio {
		namespace {
		static constexpr const char BlasrGitSha1Int[] = "@BLASR_GIT_SHA1@";
		}

		inline std::string BlasrGitSha1()
		{
		if (sizeof(BlasrGitSha1Int) == 1) {
		// corresponds to a release
		return std::string();
		} else {
		// we have a git SHA1
		return std::string("-") + BlasrGitSha1Int;
		}
		}

		} // ::PacBio