bio-samtools-wrapper 2.7.0

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  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.travis.yml +27 -0
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  5. data/LICENSE.txt +702 -0
  6. data/README.md +501 -0
  7. data/Rakefile +73 -0
  8. data/VERSION +1 -0
  9. data/bin/bam_consensus.rb +85 -0
  10. data/bio-samtools-wrapper.gemspec +181 -0
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  63. data/ext/Makefile-bioruby.patch +12 -0
  64. data/ext/Makefile-suse.patch +11 -0
  65. data/ext/mkrf_conf.rb +118 -0
  66. data/lib/bio/BIOExtensions.rb +89 -0
  67. data/lib/bio/db/alignment.rb +64 -0
  68. data/lib/bio/db/fastadb.rb +320 -0
  69. data/lib/bio/db/pileup.rb +273 -0
  70. data/lib/bio/db/sam/external/COPYING +21 -0
  71. data/lib/bio/db/sam/external/VERSION +1 -0
  72. data/lib/bio/db/sam/library.rb +32 -0
  73. data/lib/bio/db/sam.rb +778 -0
  74. data/lib/bio/db/vcf.rb +105 -0
  75. data/lib/bio-samtools-wrapper.rb +9 -0
  76. data/test/.gitignore +1 -0
  77. data/test/helper.rb +18 -0
  78. data/test/sample.vcf +24 -0
  79. data/test/samples/.gitignore +1 -0
  80. data/test/samples/LCI/NC_001988.ffn +2 -0
  81. data/test/samples/LCI/test.bam +0 -0
  82. data/test/samples/LCI/test.bam.bai +0 -0
  83. data/test/samples/small/dupes.bam +0 -0
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  108. data/test/samples/small/test_chr.fasta.rev.1.bt2 +0 -0
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  113. data/test/samples/small/test_cov.svg +273 -0
  114. data/test/samples/small/test_fastadb.fasta +34 -0
  115. data/test/samples/small/testu.bam +0 -0
  116. data/test/samples/small/testu.bed +2 -0
  117. data/test/test_bio-samtools-wrapper.rb +1 -0
  118. data/test/test_fastadb.rb +89 -0
  119. data/test/test_pileup.rb +90 -0
  120. data/test/test_sam.rb +421 -0
  121. data/test/test_vcf.rb +79 -0
  122. data/tutorial/tutorial.html +474 -0
  123. data/tutorial/tutorial.md +424 -0
  124. data/tutorial/tutorial.pdf +0 -0
  125. metadata +254 -0
data/LICENSE.txt ADDED
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+ Corresponding Source conveyed, and Installation Information provided,
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+ 7. Additional Terms.
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+
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+ "Additional permissions" are terms that supplement the terms of this
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+ Additional permissions that are applicable to the entire Program shall
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+ that they are valid under applicable law. If additional permissions
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+ apply only to part of the Program, that part may be used separately
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+ under those permissions, but the entire Program remains governed by
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+ When you convey a copy of a covered work, you may at your option
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+ remove any additional permissions from that copy, or from any part of
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+ it. (Additional permissions may be written to require their own
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+ Notwithstanding any other provision of this License, for material you
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+ b) Requiring preservation of specified reasonable legal notices or
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+ All other non-permissive additional terms are considered "further
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+ restrictions" within the meaning of section 10. If the Program as you
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+ Additional terms, permissive or non-permissive, may be stated in the
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+ the above requirements apply either way.
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+
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+ 8. Termination.
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+
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+ You may not propagate or modify a covered work except as expressly
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+ However, if you cease all violation of this License, then your
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+ Moreover, your license from a particular copyright holder is
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+ Termination of your rights under this section does not terminate the
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+ this License. If your rights have been terminated and not permanently
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+ reinstated, you do not qualify to receive new licenses for the same
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+ material under section 10.
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+
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+ 9. Acceptance Not Required for Having Copies.
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+
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+ You are not required to accept this License in order to receive or
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+ run a copy of the Program. Ancillary propagation of a covered work
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+ occurring solely as a consequence of using peer-to-peer transmission
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+ to receive a copy likewise does not require acceptance. However,
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+ nothing other than this License grants you permission to propagate or
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+ covered work, you indicate your acceptance of this License to do so.
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+ 10. Automatic Licensing of Downstream Recipients.
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+
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+ Each time you convey a covered work, the recipient automatically
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+ receives a license from the original licensors, to run, modify and
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+ propagate that work, subject to this License. You are not responsible
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+ An "entity transaction" is a transaction transferring control of an
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+ You may not impose any further restrictions on the exercise of the
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+ any patent claim is infringed by making, using, selling, offering for
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+ sale, or importing the Program or any portion of it.
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+
499
+ 11. Patents.
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+
501
+ A "contributor" is a copyright holder who authorizes use under this
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+ License of the Program or a work on which the Program is based. The
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+ work thus licensed is called the contributor's "contributor version".
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+
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+ A contributor's "essential patent claims" are all patent claims
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+ owned or controlled by the contributor, whether already acquired or
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+ hereafter acquired, that would be infringed by some manner, permitted
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+ but do not include claims that would be infringed only as a
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+ consequence of further modification of the contributor version. For
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+ purposes of this definition, "control" includes the right to grant
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+ patent sublicenses in a manner consistent with the requirements of
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+ Each contributor grants you a non-exclusive, worldwide, royalty-free
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+ patent license under the contributor's essential patent claims, to
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+ propagate the contents of its contributor version.
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+
520
+ In the following three paragraphs, a "patent license" is any express
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+ agreement or commitment, however denominated, not to enforce a patent
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+ (such as an express permission to practice a patent or covenant not to
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+ sue for patent infringement). To "grant" such a patent license to a
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+ patent against the party.
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+
527
+ If you convey a covered work, knowingly relying on a patent license,
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+ and the Corresponding Source of the work is not available for anyone
529
+ to copy, free of charge and under the terms of this License, through a
530
+ publicly available network server or other readily accessible means,
531
+ then you must either (1) cause the Corresponding Source to be so
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+ available, or (2) arrange to deprive yourself of the benefit of the
533
+ patent license for this particular work, or (3) arrange, in a manner
534
+ consistent with the requirements of this License, to extend the patent
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+ license to downstream recipients. "Knowingly relying" means you have
536
+ actual knowledge that, but for the patent license, your conveying the
537
+ covered work in a country, or your recipient's use of the covered work
538
+ in a country, would infringe one or more identifiable patents in that
539
+ country that you have reason to believe are valid.
540
+
541
+ If, pursuant to or in connection with a single transaction or
542
+ arrangement, you convey, or propagate by procuring conveyance of, a
543
+ covered work, and grant a patent license to some of the parties
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+ receiving the covered work authorizing them to use, propagate, modify
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+ or convey a specific copy of the covered work, then the patent license
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+ you grant is automatically extended to all recipients of the covered
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+ work and works based on it.
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+
549
+ A patent license is "discriminatory" if it does not include within
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+ the scope of its coverage, prohibits the exercise of, or is
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+ conditioned on the non-exercise of one or more of the rights that are
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+ specifically granted under this License. You may not convey a covered
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+ work if you are a party to an arrangement with a third party that is
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+ in the business of distributing software, under which you make payment
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+ to the third party based on the extent of your activity of conveying
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+ the work, and under which the third party grants, to any of the
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+ parties who would receive the covered work from you, a discriminatory
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+ patent license (a) in connection with copies of the covered work
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+ conveyed by you (or copies made from those copies), or (b) primarily
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+ for and in connection with specific products or compilations that
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+ contain the covered work, unless you entered into that arrangement,
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+ or that patent license was granted, prior to 28 March 2007.
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+
564
+ Nothing in this License shall be construed as excluding or limiting
565
+ any implied license or other defenses to infringement that may
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+ otherwise be available to you under applicable patent law.
567
+
568
+ 12. No Surrender of Others' Freedom.
569
+
570
+ If conditions are imposed on you (whether by court order, agreement or
571
+ otherwise) that contradict the conditions of this License, they do not
572
+ excuse you from the conditions of this License. If you cannot convey a
573
+ covered work so as to satisfy simultaneously your obligations under this
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+ License and any other pertinent obligations, then as a consequence you may
575
+ not convey it at all. For example, if you agree to terms that obligate you
576
+ to collect a royalty for further conveying from those to whom you convey
577
+ the Program, the only way you could satisfy both those terms and this
578
+ License would be to refrain entirely from conveying the Program.
579
+
580
+ 13. Use with the GNU Affero General Public License.
581
+
582
+ Notwithstanding any other provision of this License, you have
583
+ permission to link or combine any covered work with a work licensed
584
+ under version 3 of the GNU Affero General Public License into a single
585
+ combined work, and to convey the resulting work. The terms of this
586
+ License will continue to apply to the part which is the covered work,
587
+ but the special requirements of the GNU Affero General Public License,
588
+ section 13, concerning interaction through a network will apply to the
589
+ combination as such.
590
+
591
+ 14. Revised Versions of this License.
592
+
593
+ The Free Software Foundation may publish revised and/or new versions of
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+ the GNU General Public License from time to time. Such new versions will
595
+ be similar in spirit to the present version, but may differ in detail to
596
+ address new problems or concerns.
597
+
598
+ Each version is given a distinguishing version number. If the
599
+ Program specifies that a certain numbered version of the GNU General
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+ Public License "or any later version" applies to it, you have the
601
+ option of following the terms and conditions either of that numbered
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+ version or of any later version published by the Free Software
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+ Foundation. If the Program does not specify a version number of the
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+ GNU General Public License, you may choose any version ever published
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+ by the Free Software Foundation.
606
+
607
+ If the Program specifies that a proxy can decide which future
608
+ versions of the GNU General Public License can be used, that proxy's
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+ public statement of acceptance of a version permanently authorizes you
610
+ to choose that version for the Program.
611
+
612
+ Later license versions may give you additional or different
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+ permissions. However, no additional obligations are imposed on any
614
+ author or copyright holder as a result of your choosing to follow a
615
+ later version.
616
+
617
+ 15. Disclaimer of Warranty.
618
+
619
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
620
+ APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
621
+ HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
622
+ OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
623
+ THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
624
+ PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
625
+ IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
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+ ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
627
+
628
+ 16. Limitation of Liability.
629
+
630
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
631
+ WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
632
+ THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
633
+ GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
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+ USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
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+ DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
636
+ PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
637
+ EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
638
+ SUCH DAMAGES.
639
+
640
+ 17. Interpretation of Sections 15 and 16.
641
+
642
+ If the disclaimer of warranty and limitation of liability provided
643
+ above cannot be given local legal effect according to their terms,
644
+ reviewing courts shall apply local law that most closely approximates
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+ an absolute waiver of all civil liability in connection with the
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+ Program, unless a warranty or assumption of liability accompanies a
647
+ copy of the Program in return for a fee.
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+
649
+ END OF TERMS AND CONDITIONS
650
+
651
+ How to Apply These Terms to Your New Programs
652
+
653
+ If you develop a new program, and you want it to be of the greatest
654
+ possible use to the public, the best way to achieve this is to make it
655
+ free software which everyone can redistribute and change under these terms.
656
+
657
+ To do so, attach the following notices to the program. It is safest
658
+ to attach them to the start of each source file to most effectively
659
+ state the exclusion of warranty; and each file should have at least
660
+ the "copyright" line and a pointer to where the full notice is found.
661
+
662
+ <one line to give the program's name and a brief idea of what it does.>
663
+ Copyright (C) <year> <name of author>
664
+
665
+ This program is free software: you can redistribute it and/or modify
666
+ it under the terms of the GNU General Public License as published by
667
+ the Free Software Foundation, either version 3 of the License, or
668
+ (at your option) any later version.
669
+
670
+ This program is distributed in the hope that it will be useful,
671
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
672
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
673
+ GNU General Public License for more details.
674
+
675
+ You should have received a copy of the GNU General Public License
676
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
677
+
678
+ Also add information on how to contact you by electronic and paper mail.
679
+
680
+ If the program does terminal interaction, make it output a short
681
+ notice like this when it starts in an interactive mode:
682
+
683
+ <program> Copyright (C) <year> <name of author>
684
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
685
+ This is free software, and you are welcome to redistribute it
686
+ under certain conditions; type `show c' for details.
687
+
688
+ The hypothetical commands `show w' and `show c' should show the appropriate
689
+ parts of the General Public License. Of course, your program's commands
690
+ might be different; for a GUI interface, you would use an "about box".
691
+
692
+ You should also get your employer (if you work as a programmer) or school,
693
+ if any, to sign a "copyright disclaimer" for the program, if necessary.
694
+ For more information on this, and how to apply and follow the GNU GPL, see
695
+ <http://www.gnu.org/licenses/>.
696
+
697
+ The GNU General Public License does not permit incorporating your program
698
+ into proprietary programs. If your program is a subroutine library, you
699
+ may consider it more useful to permit linking proprietary applications with
700
+ the library. If this is what you want to do, use the GNU Lesser General
701
+ Public License instead of this License. But first, please read
702
+ <http://www.gnu.org/philosophy/why-not-lgpl.html>.