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‎LICENSE‎

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Artistic License 2.0
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Preamble
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This license establishes the terms under which a given free software
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Package may be copied, modified, distributed, and/or redistributed. The
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intent is that the Copyright Holder maintains some artistic control over
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the development of that Package while still keeping the Package
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available as open source and free software.
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You are always permitted to make arrangements wholly outside of this
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license directly with the Copyright Holder of a given Package. If the
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terms of this license do not permit the full use that you propose to
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make of the Package, you should contact the Copyright Holder and seek a
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different licensing arrangement. Definitions
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"Copyright Holder" means the individual(s) or organization(s) named in
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the copyright notice for the entire Package.
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"Contributor" means any party that has contributed code or other
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material to the Package, in accordance with the Copyright Holder's
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procedures.
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"You" and "your" means any person who would like to copy, distribute, or
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modify the Package.
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"Package" means the collection of files distributed by the Copyright
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Holder, and derivatives of that collection and/or of those files. A
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given Package may consist of either the Standard Version, or a Modified
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Version.
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"Distribute" means providing a copy of the Package or making it
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accessible to anyone else, or in the case of a company or organization,
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to others outside of your company or organization.
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"Distributor Fee" means any fee that you charge for Distributing this
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Package or providing support for this Package to another party. It does
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not mean licensing fees.
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"Standard Version" refers to the Package if it has not been modified, or
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has been modified only in ways explicitly requested by the Copyright
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Holder.
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"Modified Version" means the Package, if it has been changed, and such
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changes were not explicitly requested by the Copyright Holder.
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"Original License" means this Artistic License as Distributed with the
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Standard Version of the Package, in its current version or as it may be
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modified by The Perl Foundation in the future.
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"Source" form means the source code, documentation source, and
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configuration files for the Package.
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"Compiled" form means the compiled bytecode, object code, binary, or any
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other form resulting from mechanical transformation or translation of
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the Source form. Permission for Use and Modification Without
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Distribution
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(1) You are permitted to use the Standard Version and create and use
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Modified Versions for any purpose without restriction, provided that you
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do not Distribute the Modified Version. Permissions for Redistribution
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of the Standard Version
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(2) You may Distribute verbatim copies of the Source form of the
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Standard Version of this Package in any medium without restriction,
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either gratis or for a Distributor Fee, provided that you duplicate all
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of the original copyright notices and associated disclaimers. At your
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discretion, such verbatim copies may or may not include a Compiled form
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of the Package.
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(3) You may apply any bug fixes, portability changes, and other
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modifications made available from the Copyright Holder. The resulting
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Package will still be considered the Standard Version, and as such will
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be subject to the Original License. Distribution of Modified Versions of
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the Package as Source
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(4) You may Distribute your Modified Version as Source (either gratis or
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for a Distributor Fee, and with or without a Compiled form of the
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Modified Version) provided that you clearly document how it differs from
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the Standard Version, including, but not limited to, documenting any
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non-standard features, executables, or modules, and provided that you do
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at least ONE of the following:
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(a) make the Modified Version available to the Copyright Holder of the
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Standard Version, under the Original License, so that the Copyright
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Holder may include your modifications in the Standard Version. (b)
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ensure that installation of your Modified Version does not prevent the
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user installing or running the Standard Version. In addition, the
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Modified Version must bear a name that is different from the name of the
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Standard Version. (c) allow anyone who receives a copy of the Modified
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Version to make the Source form of the Modified Version available to
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others under (i) the Original License or (ii) a license that permits the
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licensee to freely copy, modify and redistribute the Modified Version
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using the same licensing terms that apply to the copy that the licensee
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received, and requires that the Source form of the Modified Version, and
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of any works derived from it, be made freely available in that license
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fees are prohibited but Distributor Fees are allowed. Distribution of
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Compiled Forms of the Standard Version or Modified Versions without the
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Source
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(5) You may Distribute Compiled forms of the Standard Version without
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the Source, provided that you include complete instructions on how to
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get the Source of the Standard Version. Such instructions must be valid
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at the time of your distribution. If these instructions, at any time
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while you are carrying out such distribution, become invalid, you must
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provide new instructions on demand or cease further distribution. If you
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provide valid instructions or cease distribution within thirty days
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after you become aware that the instructions are invalid, then you do
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not forfeit any of your rights under this license.
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(6) You may Distribute a Modified Version in Compiled form without the
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Source, provided that you comply with Section 4 with respect to the
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Source of the Modified Version. Aggregating or Linking the Package
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(7) You may aggregate the Package (either the Standard Version or
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Modified Version) with other packages and Distribute the resulting
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aggregation provided that you do not charge a licensing fee for the
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Package. Distributor Fees are permitted, and licensing fees for other
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components in the aggregation are permitted. The terms of this license
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apply to the use and Distribution of the Standard or Modified Versions
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as included in the aggregation.
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(8) You are permitted to link Modified and Standard Versions with other
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works, to embed the Package in a larger work of your own, or to build
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stand-alone binary or bytecode versions of applications that include the
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Package, and Distribute the result without restriction, provided the
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result does not expose a direct interface to the Package. Items That are
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Not Considered Part of a Modified Version
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(9) Works (including, but not limited to, modules and scripts) that
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merely extend or make use of the Package, do not, by themselves, cause
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the Package to be a Modified Version. In addition, such works are not
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considered parts of the Package itself, and are not subject to the terms
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of this license. General Provisions
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(10) Any use, modification, and distribution of the Standard or Modified
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Versions is governed by this Artistic License. By using, modifying or
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distributing the Package, you accept this license. Do not use, modify,
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or distribute the Package, if you do not accept this license.
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(11) If your Modified Version has been derived from a Modified Version
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made by someone other than you, you are nevertheless required to ensure
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that your Modified Version complies with the requirements of this
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license.
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(12) This license does not grant you the right to use any trademark,
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service mark, tradename, or logo of the Copyright Holder.
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(13) This license includes the non-exclusive, worldwide, free-of-charge
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patent license to make, have made, use, offer to sell, sell, import and
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otherwise transfer the Package with respect to any patent claims
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licensable by the Copyright Holder that are necessarily infringed by the
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Package. If you institute patent litigation (including a cross-claim or
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counterclaim) against any party alleging that the Package constitutes
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direct or contributory patent infringement, then this Artistic License
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to you shall terminate on the date that such litigation is filed.
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(14) Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT
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HOLDER AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED
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WARRANTIES. THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
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PARTICULAR PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT
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PERMITTED BY YOUR LOCAL LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER
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OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR
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CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE,
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EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

‎Makefile‎

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BAM := ./samtools-0.1.18
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#path to the directory where the samtools package was built (in place)
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#so libbam.a and *.h files MUST be in here
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GDIR := ./gclib
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SEARCHDIRS := -I. -I${GDIR} -I${BAM}
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#SYSTYPE := $(shell uname)
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CC := g++
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ifneq (,$(findstring nothreads,$(MAKECMDGOALS)))
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NOTHREADS=1
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endif
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#detect MinGW (Windows environment)
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ifneq (,$(findstring mingw,$(shell ${CC} -dumpmachine)))
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WINDOWS=1
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endif
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LFLAGS =
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# MinGW32 GCC 4.5 link problem fix
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#ifdef WINDOWS
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ifneq (,$(findstring 4.5.,$(shell g++ -dumpversion)))
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LFLAGS += -static-libstdc++ -static-libgcc
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endif
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#endif
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# Misc. system commands
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ifdef WINDOWS
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RM = del /Q
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else
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RM = rm -f
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endif
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# File endings
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ifdef WINDOWS
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EXE = .exe
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else
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EXE =
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endif
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BASEFLAGS := -Wall -Wextra ${SEARCHDIRS} $(MARCH) -D_FILE_OFFSET_BITS=64 \
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-D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti
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# C/C++ linker
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LINKER := g++
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LIBS := -lbam -lz
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# Non-windows systems need pthread
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ifndef WINDOWS
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#ifndef NOTHREADS
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# unfortunately the new samtools requires pthread anyway
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LIBS += -lpthread
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#endif
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endif
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ifdef NOTHREADS
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BASEFLAGS += -DNOTHREADS
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endif
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###----- generic build rule
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ifneq (,$(findstring release,$(MAKECMDGOALS)))
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CFLAGS := -O2 -DNDEBUG -g $(BASEFLAGS)
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LDFLAGS := -g -L${BAM} ${LFLAGS}
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else
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CFLAGS := -g -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS)
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LDFLAGS := -g -L${BAM}
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GDEBUG = 1
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endif
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%.o : %.cpp
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${CC} ${CFLAGS} -c $< -o $@
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OBJS := ${GDIR}/GBase.o ${GDIR}/GArgs.o ${GDIR}/GStr.o ${GDIR}/GBam.o \
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${GDIR}/gdna.o ${GDIR}/codons.o ${GDIR}/GFaSeqGet.o ${GDIR}/gff.o
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ifndef NOTHREADS
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OBJS += ${GDIR}/GThreads.o
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endif
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ifdef GDEBUG
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OBJS += ${GDIR}/proc_mem.o
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endif
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OBJS += rlink.o
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.PHONY : all debug clean release nothreads
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all: stringtie
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release: stringtie
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debug: stringtie
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nothreads: stringtie
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${GDIR}/GBam.o : $(GDIR)/GBam.h
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stringtie.o : $(GDIR)/GBitVec.h $(GDIR)/GHash.hh $(GDIR)/GBam.h
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rlink.o : rlink.h $(GDIR)/GBam.h $(GDIR)/GBitVec.h
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${BAM}/libbam.a:
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cd ${BAM} && make lib
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stringtie: ${BAM}/libbam.a $(OBJS) stringtie.o
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${LINKER} ${LDFLAGS} -o $@ ${filter-out %.a %.so, $^} ${LIBS}
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# target for removing all object files
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clean:
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cd ${BAM} && make clean
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@${RM} stringtie stringtie.o* stringtie.exe $(OBJS)
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@${RM} core.*
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