[med-svn] [Git][med-team/ffindex][upstream] New upstream version 0.9.9.9
Andreas Tille
gitlab at salsa.debian.org
Mon Jan 28 18:08:19 GMT 2019
Andreas Tille pushed to branch upstream at Debian Med / ffindex
Commits:
4d1c7063 by Andreas Tille at 2019-01-28T17:58:43Z
New upstream version 0.9.9.9
- - - - -
19 changed files:
- LICENSE
- README
- RELEASE_NOTES
- VERSION
- rpm/ffindex.spec
- src/Makefile
- src/ffindex.c
- src/ffindex.h
- src/ffindex_apply_mpi.c
- src/ffindex_apply_mpi_spawn.c
- src/ffindex_build.c
- src/ffindex_from_fasta.c
- src/ffindex_from_tsv.c
- src/ffindex_get.c
- src/ffindex_modify.c
- src/ffindex_optimize.c
- src/ffindex_unpack.c
- src/ffutil.c
- src/ffutil.h
Changes:
=====================================
LICENSE
=====================================
@@ -1,346 +1,428 @@
-AUTHOR
-
-FFindex was designed and implemented by Andreas Hauser <andy at splashground.de>.
-Please add your name here if you distribute modified versions.
-
-This file must be distributed with any source or binary distribution including
-parts of this work, excempt ffutil.h and ffutil.c which are also available
-under MIT license.
-
-SHORT SUMMARY OF THE LICENSE
-
-FFindex is provided under the Create Commons license "Attribution-ShareAlike
-3.0", which basically captures the spirit of the Gnu Public License (GPL).
-
-See:
-http://creativecommons.org/licenses/by-sa/3.0/
-
-Basically you are free:
-
- * to Share — to copy, distribute and transmit the work
- * to Remix — to adapt the work
-
-Under the following conditions:
-
- * Attribution
- You must attribute the work in the manner specified by the author or
- licensor (but not in any way that suggests that they endorse you or your
- use of the work).
- * Share Alike
- If you alter, transform, or build upon this work, you may distribute the
- resulting work only under the same or similar license to this one.
-
-
-LICENSE
-
-THE WORK (AS DEFINED BELOW) IS PROVIDED UNDER THE TERMS OF THIS CREATIVE
-COMMONS PUBLIC LICENSE ("CCPL" OR "LICENSE"). THE WORK IS PROTECTED BY
-COPYRIGHT AND/OR OTHER APPLICABLE LAW. ANY USE OF THE WORK OTHER THAN AS
-AUTHORIZED UNDER THIS LICENSE OR COPYRIGHT LAW IS PROHIBITED.
-
-BY EXERCISING ANY RIGHTS TO THE WORK PROVIDED HERE, YOU ACCEPT AND AGREE TO BE
-BOUND BY THE TERMS OF THIS LICENSE. TO THE EXTENT THIS LICENSE MAY BE
-CONSIDERED TO BE A CONTRACT, THE LICENSOR GRANTS YOU THE RIGHTS CONTAINED HERE
-IN CONSIDERATION OF YOUR ACCEPTANCE OF SUCH TERMS AND CONDITIONS.
-
-1. Definitions
-
- 1. "Adaptation" means a work based upon the Work, or upon the Work and other
- pre-existing works, such as a translation, adaptation, derivative work,
- arrangement of music or other alterations of a literary or artistic work,
- or phonogram or performance and includes cinematographic adaptations or
- any other form in which the Work may be recast, transformed, or adapted
- including in any form recognizably derived from the original, except that
- a work that constitutes a Collection will not be considered an Adaptation
- for the purpose of this License. For the avoidance of doubt, where the
- Work is a musical work, performance or phonogram, the synchronization of
- the Work in timed-relation with a moving image ("synching") will be
- considered an Adaptation for the purpose of this License.
- 2. "Collection" means a collection of literary or artistic works, such as
- encyclopedias and anthologies, or performances, phonograms or broadcasts,
- or other works or subject matter other than works listed in Section 1(f)
- below, which, by reason of the selection and arrangement of their
- contents, constitute intellectual creations, in which the Work is
- included in its entirety in unmodified form along with one or more other
- contributions, each constituting separate and independent works in
- themselves, which together are assembled into a collective whole. A work
- that constitutes a Collection will not be considered an Adaptation (as
- defined below) for the purposes of this License.
- 3. "Creative Commons Compatible License" means a license that is listed at
- http://creativecommons.org/compatiblelicenses that has been approved by
- Creative Commons as being essentially equivalent to this License,
- including, at a minimum, because that license: (i) contains terms that
- have the same purpose, meaning and effect as the License Elements of this
- License; and, (ii) explicitly permits the relicensing of adaptations of
- works made available under that license under this License or a Creative
- Commons jurisdiction license with the same License Elements as this
- License.
- 4. "Distribute" means to make available to the public the original and
- copies of the Work or Adaptation, as appropriate, through sale or other
- transfer of ownership.
- 5. "License Elements" means the following high-level license attributes as
- selected by Licensor and indicated in the title of this License:
- Attribution, ShareAlike.
- 6. "Licensor" means the individual, individuals, entity or entities that
- offer(s) the Work under the terms of this License.
- 7. "Original Author" means, in the case of a literary or artistic work, the
- individual, individuals, entity or entities who created the Work or if no
- individual or entity can be identified, the publisher; and in addition
- (i) in the case of a performance the actors, singers, musicians, dancers,
- and other persons who act, sing, deliver, declaim, play in, interpret or
- otherwise perform literary or artistic works or expressions of folklore;
- (ii) in the case of a phonogram the producer being the person or legal
- entity who first fixes the sounds of a performance or other sounds; and,
- (iii) in the case of broadcasts, the organization that transmits the
- broadcast.
- 8. "Work" means the literary and/or artistic work offered under the terms of
- this License including without limitation any production in the literary,
- scientific and artistic domain, whatever may be the mode or form of its
- expression including digital form, such as a book, pamphlet and other
- writing; a lecture, address, sermon or other work of the same nature; a
- dramatic or dramatico-musical work; a choreographic work or entertainment
- in dumb show; a musical composition with or without words; a
- cinematographic work to which are assimilated works expressed by a
- process analogous to cinematography; a work of drawing, painting,
- architecture, sculpture, engraving or lithography; a photographic work to
- which are assimilated works expressed by a process analogous to
- photography; a work of applied art; an illustration, map, plan, sketch or
- three-dimensional work relative to geography, topography, architecture or
- science; a performance; a broadcast; a phonogram; a compilation of data
- to the extent it is protected as a copyrightable work; or a work
- performed by a variety or circus performer to the extent it is not
- otherwise considered a literary or artistic work.
- 9. "You" means an individual or entity exercising rights under this License
- who has not previously violated the terms of this License with respect to
- the Work, or who has received express permission from the Licensor to
- exercise rights under this License despite a previous violation.
- 10. "Publicly Perform" means to perform public recitations of the Work and to
- communicate to the public those public recitations, by any means or
- process, including by wire or wireless means or public digital
- performances; to make available to the public Works in such a way that
- members of the public may access these Works from a place and at a place
- individually chosen by them; to perform the Work to the public by any
- means or process and the communication to the public of the performances
- of the Work, including by public digital performance; to broadcast and
- rebroadcast the Work by any means including signs, sounds or images.
- 11. "Reproduce" means to make copies of the Work by any means including
- without limitation by sound or visual recordings and the right of
- fixation and reproducing fixations of the Work, including storage of a
- protected performance or phonogram in digital form or other electronic
- medium.
-
-2. Fair Dealing Rights. Nothing in this License is intended to reduce, limit,
- or restrict any uses free from copyright or rights arising from limitations
- or exceptions that are provided for in connection with the copyright
- protection under copyright law or other applicable laws.
-
-3. License Grant. Subject to the terms and conditions of this License, Licensor
- hereby grants You a worldwide, royalty-free, non-exclusive, perpetual (for
- the duration of the applicable copyright) license to exercise the rights in
- the Work as stated below:
-
- 1. to Reproduce the Work, to incorporate the Work into one or more
- Collections, and to Reproduce the Work as incorporated in the
- Collections;
- 2. to create and Reproduce Adaptations provided that any such Adaptation,
- including any translation in any medium, takes reasonable steps to
- clearly label, demarcate or otherwise identify that changes were made to
- the original Work. For example, a translation could be marked "The
- original work was translated from English to Spanish," or a modification
- could indicate "The original work has been modified.";
- 3. to Distribute and Publicly Perform the Work including as incorporated in
- Collections; and,
- 4. to Distribute and Publicly Perform Adaptations.
- 5.
- For the avoidance of doubt:
- 1. Non-waivable Compulsory License Schemes. In those jurisdictions in
- which the right to collect royalties through any statutory or
- compulsory licensing scheme cannot be waived, the Licensor reserves
- the exclusive right to collect such royalties for any exercise by
- You of the rights granted under this License;
- 2. Waivable Compulsory License Schemes. In those jurisdictions in
- which the right to collect royalties through any statutory or
- compulsory licensing scheme can be waived, the Licensor waives the
- exclusive right to collect such royalties for any exercise by You
- of the rights granted under this License; and,
- 3. Voluntary License Schemes. The Licensor waives the right to collect
- royalties, whether individually or, in the event that the Licensor
- is a member of a collecting society that administers voluntary
- licensing schemes, via that society, from any exercise by You of
- the rights granted under this License.
-
-The above rights may be exercised in all media and formats whether now known or
-hereafter devised. The above rights include the right to make such
-modifications as are technically necessary to exercise the rights in other
-media and formats. Subject to Section 8(f), all rights not expressly granted by
-Licensor are hereby reserved.
-
-4. Restrictions.
-The license granted in Section 3 above is expressly made subject to and limited
-by the following restrictions:
-
- 1. You may Distribute or Publicly Perform the Work only under the terms of
- this License. You must include a copy of, or the Uniform Resource
- Identifier (URI) for, this License with every copy of the Work You
- Distribute or Publicly Perform. You may not offer or impose any terms on
- the Work that restrict the terms of this License or the ability of the
- recipient of the Work to exercise the rights granted to that recipient
- under the terms of the License. You may not sublicense the Work. You must
- keep intact all notices that refer to this License and to the disclaimer
- of warranties with every copy of the Work You Distribute or Publicly
- Perform. When You Distribute or Publicly Perform the Work, You may not
- impose any effective technological measures on the Work that restrict the
- ability of a recipient of the Work from You to exercise the rights
- granted to that recipient under the terms of the License. This Section
- 4(a) applies to the Work as incorporated in a Collection, but this does
- not require the Collection apart from the Work itself to be made subject
- to the terms of this License. If You create a Collection, upon notice
- from any Licensor You must, to the extent practicable, remove from the
- Collection any credit as required by Section 4(c), as requested. If You
- create an Adaptation, upon notice from any Licensor You must, to the
- extent practicable, remove from the Adaptation any credit as required by
- Section 4(c), as requested.
- 2. You may Distribute or Publicly Perform an Adaptation only under the terms
- of: (i) this License; (ii) a later version of this License with the same
- License Elements as this License; (iii) a Creative Commons jurisdiction
- license (either this or a later license version) that contains the same
- License Elements as this License (e.g., Attribution-ShareAlike 3.0 US));
- (iv) a Creative Commons Compatible License. If you license the Adaptation
- under one of the licenses mentioned in (iv), you must comply with the
- terms of that license. If you license the Adaptation under the terms of
- any of the licenses mentioned in (i), (ii) or (iii) (the "Applicable
- License"), you must comply with the terms of the Applicable License
- generally and the following provisions: (I) You must include a copy of,
- or the URI for, the Applicable License with every copy of each Adaptation
- You Distribute or Publicly Perform; (II) You may not offer or impose any
- terms on the Adaptation that restrict the terms of the Applicable License
- or the ability of the recipient of the Adaptation to exercise the rights
- granted to that recipient under the terms of the Applicable License;
- (III) You must keep intact all notices that refer to the Applicable
- License and to the disclaimer of warranties with every copy of the Work
- as included in the Adaptation You Distribute or Publicly Perform; (IV)
- when You Distribute or Publicly Perform the Adaptation, You may not
- impose any effective technological measures on the Adaptation that
- restrict the ability of a recipient of the Adaptation from You to
- exercise the rights granted to that recipient under the terms of the
- Applicable License. This Section 4(b) applies to the Adaptation as
- incorporated in a Collection, but this does not require the Collection
- apart from the Adaptation itself to be made subject to the terms of the
- Applicable License.
- 3. If You Distribute, or Publicly Perform the Work or any Adaptations or
- Collections, You must, unless a request has been made pursuant to Section
- 4(a), keep intact all copyright notices for the Work and provide,
- reasonable to the medium or means You are utilizing: (i) the name of the
- Original Author (or pseudonym, if applicable) if supplied, and/or if the
- Original Author and/or Licensor designate another party or parties (e.g.,
- a sponsor institute, publishing entity, journal) for attribution
- ("Attribution Parties") in Licensor's copyright notice, terms of service
- or by other reasonable means, the name of such party or parties; (ii) the
- title of the Work if supplied; (iii) to the extent reasonably
- practicable, the URI, if any, that Licensor specifies to be associated
- with the Work, unless such URI does not refer to the copyright notice or
- licensing information for the Work; and (iv) , consistent with Ssection
- 3(b), in the case of an Adaptation, a credit identifying the use of the
- Work in the Adaptation (e.g., "French translation of the Work by Original
- Author," or "Screenplay based on original Work by Original Author"). The
- credit required by this Section 4(c) may be implemented in any reasonable
- manner; provided, however, that in the case of a Adaptation or
- Collection, at a minimum such credit will appear, if a credit for all
- contributing authors of the Adaptation or Collection appears, then as
- part of these credits and in a manner at least as prominent as the
- credits for the other contributing authors. For the avoidance of doubt,
- You may only use the credit required by this Section for the purpose of
- attribution in the manner set out above and, by exercising Your rights
- under this License, You may not implicitly or explicitly assert or imply
- any connection with, sponsorship or endorsement by the Original Author,
- Licensor and/or Attribution Parties, as appropriate, of You or Your use
- of the Work, without the separate, express prior written permission of
- the Original Author, Licensor and/or Attribution Parties.
- 4. Except as otherwise agreed in writing by the Licensor or as may be
- otherwise permitted by applicable law, if You Reproduce, Distribute or
- Publicly Perform the Work either by itself or as part of any Adaptations
- or Collections, You must not distort, mutilate, modify or take other
- derogatory action in relation to the Work which would be prejudicial to
- the Original Author's honor or reputation. Licensor agrees that in those
- jurisdictions (e.g. Japan), in which any exercise of the right granted in
- Section 3(b) of this License (the right to make Adaptations) would be
- deemed to be a distortion, mutilation, modification or other derogatory
- action prejudicial to the Original Author's honor and reputation, the
- Licensor will waive or not assert, as appropriate, this Section, to the
- fullest extent permitted by the applicable national law, to enable You to
- reasonably exercise Your right under Section 3(b) of this License (right
- to make Adaptations) but not otherwise.
-
-5. Representations, Warranties and Disclaimer
-
-UNLESS OTHERWISE MUTUALLY AGREED TO BY THE PARTIES IN WRITING, LICENSOR OFFERS
-THE WORK AS-IS AND MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND
-CONCERNING THE WORK, EXPRESS, IMPLIED, STATUTORY OR OTHERWISE, INCLUDING,
-WITHOUT LIMITATION, WARRANTIES OF TITLE, MERCHANTIBILITY, FITNESS FOR A
-PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS,
-ACCURACY, OR THE PRESENCE OF ABSENCE OF ERRORS, WHETHER OR NOT DISCOVERABLE.
-SOME JURISDICTIONS DO NOT ALLOW THE EXCLUSION OF IMPLIED WARRANTIES, SO SUCH
-EXCLUSION MAY NOT APPLY TO YOU.
-
-6. Limitation on Liability. EXCEPT TO THE EXTENT REQUIRED BY APPLICABLE LAW, IN
- NO EVENT WILL LICENSOR BE LIABLE TO YOU ON ANY LEGAL THEORY FOR ANY SPECIAL,
- INCIDENTAL, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES ARISING OUT OF THIS
- LICENSE OR THE USE OF THE WORK, EVEN IF LICENSOR HAS BEEN ADVISED OF THE
- POSSIBILITY OF SUCH DAMAGES.
-
-7. Termination
-
- 1. This License and the rights granted hereunder will terminate
- automatically upon any breach by You of the terms of this License.
- Individuals or entities who have received Adaptations or Collections from
- You under this License, however, will not have their licenses terminated
- provided such individuals or entities remain in full compliance with
- those licenses. Sections 1, 2, 5, 6, 7, and 8 will survive any
- termination of this License.
- 2. Subject to the above terms and conditions, the license granted here is
- perpetual (for the duration of the applicable copyright in the Work).
- Notwithstanding the above, Licensor reserves the right to release the
- Work under different license terms or to stop distributing the Work at
- any time; provided, however that any such election will not serve to
- withdraw this License (or any other license that has been, or is required
- to be, granted under the terms of this License), and this License will
- continue in full force and effect unless terminated as stated above.
-
-8. Miscellaneous
-
- 1. Each time You Distribute or Publicly Perform the Work or a Collection,
- the Licensor offers to the recipient a license to the Work on the same
- terms and conditions as the license granted to You under this License.
- 2. Each time You Distribute or Publicly Perform an Adaptation, Licensor
- offers to the recipient a license to the original Work on the same terms
- and conditions as the license granted to You under this License.
- 3. If any provision of this License is invalid or unenforceable under
- applicable law, it shall not affect the validity or enforceability of the
- remainder of the terms of this License, and without further action by the
- parties to this agreement, such provision shall be reformed to the
- minimum extent necessary to make such provision valid and enforceable.
- 4. No term or provision of this License shall be deemed waived and no breach
- consented to unless such waiver or consent shall be in writing and signed
- by the party to be charged with such waiver or consent.
- 5. This License constitutes the entire agreement between the parties with
- respect to the Work licensed here. There are no understandings,
- agreements or representations with respect to the Work not specified
- here. Licensor shall not be bound by any additional provisions that may
- appear in any communication from You. This License may not be modified
- without the mutual written agreement of the Licensor and You.
- 6. The rights granted under, and the subject matter referenced, in this
- License were drafted utilizing the terminology of the Berne Convention
- for the Protection of Literary and Artistic Works (as amended on
- September 28, 1979), the Rome Convention of 1961, the WIPO Copyright
- Treaty of 1996, the WIPO Performances and Phonograms Treaty of 1996 and
- the Universal Copyright Convention (as revised on July 24, 1971). These
- rights and subject matter take effect in the relevant jurisdiction in
- which the License terms are sought to be enforced according to the
- corresponding provisions of the implementation of those treaty provisions
- in the applicable national law. If the standard suite of rights granted
- under applicable copyright law includes additional rights not granted
- under this License, such additional rights are deemed to be included in
- the License; this License is not intended to restrict the license of any
- rights under applicable law.
+Attribution-ShareAlike 4.0 International
+=======================================================================
+
+Creative Commons Corporation ("Creative Commons") is not a law firm and
+does not provide legal services or legal advice. Distribution of
+Creative Commons public licenses does not create a lawyer-client or
+other relationship. Creative Commons makes its licenses and related
+information available on an "as-is" basis. Creative Commons gives no
+warranties regarding its licenses, any material licensed under their
+terms and conditions, or any related information. Creative Commons
+disclaims all liability for damages resulting from their use to the
+fullest extent possible.
+
+Using Creative Commons Public Licenses
+
+Creative Commons public licenses provide a standard set of terms and
+conditions that creators and other rights holders may use to share
+original works of authorship and other material subject to copyright
+and certain other rights specified in the public license below. The
+following considerations are for informational purposes only, are not
+exhaustive, and do not form part of our licenses.
+
+ Considerations for licensors: Our public licenses are
+ intended for use by those authorized to give the public
+ permission to use material in ways otherwise restricted by
+ copyright and certain other rights. Our licenses are
+ irrevocable. Licensors should read and understand the terms
+ and conditions of the license they choose before applying it.
+ Licensors should also secure all rights necessary before
+ applying our licenses so that the public can reuse the
+ material as expected. Licensors should clearly mark any
+ material not subject to the license. This includes other CC-
+ licensed material, or material used under an exception or
+ limitation to copyright. More considerations for licensors:
+ wiki.creativecommons.org/Considerations_for_licensors
+
+ Considerations for the public: By using one of our public
+ licenses, a licensor grants the public permission to use the
+ licensed material under specified terms and conditions. If
+ the licensor's permission is not necessary for any reason--for
+ example, because of any applicable exception or limitation to
+ copyright--then that use is not regulated by the license. Our
+ licenses grant only permissions under copyright and certain
+ other rights that a licensor has authority to grant. Use of
+ the licensed material may still be restricted for other
+ reasons, including because others have copyright or other
+ rights in the material. A licensor may make special requests,
+ such as asking that all changes be marked or described.
+ Although not required by our licenses, you are encouraged to
+ respect those requests where reasonable. More_considerations
+ for the public:
+ wiki.creativecommons.org/Considerations_for_licensees
+
+=======================================================================
+
+Creative Commons Attribution-ShareAlike 4.0 International Public
+License
+
+By exercising the Licensed Rights (defined below), You accept and agree
+to be bound by the terms and conditions of this Creative Commons
+Attribution-ShareAlike 4.0 International Public License ("Public
+License"). To the extent this Public License may be interpreted as a
+contract, You are granted the Licensed Rights in consideration of Your
+acceptance of these terms and conditions, and the Licensor grants You
+such rights in consideration of benefits the Licensor receives from
+making the Licensed Material available under these terms and
+conditions.
+
+
+Section 1 -- Definitions.
+
+ a. Adapted Material means material subject to Copyright and Similar
+ Rights that is derived from or based upon the Licensed Material
+ and in which the Licensed Material is translated, altered,
+ arranged, transformed, or otherwise modified in a manner requiring
+ permission under the Copyright and Similar Rights held by the
+ Licensor. For purposes of this Public License, where the Licensed
+ Material is a musical work, performance, or sound recording,
+ Adapted Material is always produced where the Licensed Material is
+ synched in timed relation with a moving image.
+
+ b. Adapter's License means the license You apply to Your Copyright
+ and Similar Rights in Your contributions to Adapted Material in
+ accordance with the terms and conditions of this Public License.
+
+ c. BY-SA Compatible License means a license listed at
+ creativecommons.org/compatiblelicenses, approved by Creative
+ Commons as essentially the equivalent of this Public License.
+
+ d. Copyright and Similar Rights means copyright and/or similar rights
+ closely related to copyright including, without limitation,
+ performance, broadcast, sound recording, and Sui Generis Database
+ Rights, without regard to how the rights are labeled or
+ categorized. For purposes of this Public License, the rights
+ specified in Section 2(b)(1)-(2) are not Copyright and Similar
+ Rights.
+
+ e. Effective Technological Measures means those measures that, in the
+ absence of proper authority, may not be circumvented under laws
+ fulfilling obligations under Article 11 of the WIPO Copyright
+ Treaty adopted on December 20, 1996, and/or similar international
+ agreements.
+
+ f. Exceptions and Limitations means fair use, fair dealing, and/or
+ any other exception or limitation to Copyright and Similar Rights
+ that applies to Your use of the Licensed Material.
+
+ g. License Elements means the license attributes listed in the name
+ of a Creative Commons Public License. The License Elements of this
+ Public License are Attribution and ShareAlike.
+
+ h. Licensed Material means the artistic or literary work, database,
+ or other material to which the Licensor applied this Public
+ License.
+
+ i. Licensed Rights means the rights granted to You subject to the
+ terms and conditions of this Public License, which are limited to
+ all Copyright and Similar Rights that apply to Your use of the
+ Licensed Material and that the Licensor has authority to license.
+
+ j. Licensor means the individual(s) or entity(ies) granting rights
+ under this Public License.
+
+ k. Share means to provide material to the public by any means or
+ process that requires permission under the Licensed Rights, such
+ as reproduction, public display, public performance, distribution,
+ dissemination, communication, or importation, and to make material
+ available to the public including in ways that members of the
+ public may access the material from a place and at a time
+ individually chosen by them.
+
+ l. Sui Generis Database Rights means rights other than copyright
+ resulting from Directive 96/9/EC of the European Parliament and of
+ the Council of 11 March 1996 on the legal protection of databases,
+ as amended and/or succeeded, as well as other essentially
+ equivalent rights anywhere in the world.
+
+ m. You means the individual or entity exercising the Licensed Rights
+ under this Public License. Your has a corresponding meaning.
+
+
+Section 2 -- Scope.
+
+ a. License grant.
+
+ 1. Subject to the terms and conditions of this Public License,
+ the Licensor hereby grants You a worldwide, royalty-free,
+ non-sublicensable, non-exclusive, irrevocable license to
+ exercise the Licensed Rights in the Licensed Material to:
+
+ a. reproduce and Share the Licensed Material, in whole or
+ in part; and
+
+ b. produce, reproduce, and Share Adapted Material.
+
+ 2. Exceptions and Limitations. For the avoidance of doubt, where
+ Exceptions and Limitations apply to Your use, this Public
+ License does not apply, and You do not need to comply with
+ its terms and conditions.
+
+ 3. Term. The term of this Public License is specified in Section
+ 6(a).
+
+ 4. Media and formats; technical modifications allowed. The
+ Licensor authorizes You to exercise the Licensed Rights in
+ all media and formats whether now known or hereafter created,
+ and to make technical modifications necessary to do so. The
+ Licensor waives and/or agrees not to assert any right or
+ authority to forbid You from making technical modifications
+ necessary to exercise the Licensed Rights, including
+ technical modifications necessary to circumvent Effective
+ Technological Measures. For purposes of this Public License,
+ simply making modifications authorized by this Section 2(a)
+ (4) never produces Adapted Material.
+
+ 5. Downstream recipients.
+
+ a. Offer from the Licensor -- Licensed Material. Every
+ recipient of the Licensed Material automatically
+ receives an offer from the Licensor to exercise the
+ Licensed Rights under the terms and conditions of this
+ Public License.
+
+ b. Additional offer from the Licensor -- Adapted Material.
+ Every recipient of Adapted Material from You
+ automatically receives an offer from the Licensor to
+ exercise the Licensed Rights in the Adapted Material
+ under the conditions of the Adapter's License You apply.
+
+ c. No downstream restrictions. You may not offer or impose
+ any additional or different terms or conditions on, or
+ apply any Effective Technological Measures to, the
+ Licensed Material if doing so restricts exercise of the
+ Licensed Rights by any recipient of the Licensed
+ Material.
+
+ 6. No endorsement. Nothing in this Public License constitutes or
+ may be construed as permission to assert or imply that You
+ are, or that Your use of the Licensed Material is, connected
+ with, or sponsored, endorsed, or granted official status by,
+ the Licensor or others designated to receive attribution as
+ provided in Section 3(a)(1)(A)(i).
+
+ b. Other rights.
+
+ 1. Moral rights, such as the right of integrity, are not
+ licensed under this Public License, nor are publicity,
+ privacy, and/or other similar personality rights; however, to
+ the extent possible, the Licensor waives and/or agrees not to
+ assert any such rights held by the Licensor to the limited
+ extent necessary to allow You to exercise the Licensed
+ Rights, but not otherwise.
+
+ 2. Patent and trademark rights are not licensed under this
+ Public License.
+
+ 3. To the extent possible, the Licensor waives any right to
+ collect royalties from You for the exercise of the Licensed
+ Rights, whether directly or through a collecting society
+ under any voluntary or waivable statutory or compulsory
+ licensing scheme. In all other cases the Licensor expressly
+ reserves any right to collect such royalties.
+
+
+Section 3 -- License Conditions.
+
+Your exercise of the Licensed Rights is expressly made subject to the
+following conditions.
+
+ a. Attribution.
+
+ 1. If You Share the Licensed Material (including in modified
+ form), You must:
+
+ a. retain the following if it is supplied by the Licensor
+ with the Licensed Material:
+
+ i. identification of the creator(s) of the Licensed
+ Material and any others designated to receive
+ attribution, in any reasonable manner requested by
+ the Licensor (including by pseudonym if
+ designated);
+
+ ii. a copyright notice;
+
+ iii. a notice that refers to this Public License;
+
+ iv. a notice that refers to the disclaimer of
+ warranties;
+
+ v. a URI or hyperlink to the Licensed Material to the
+ extent reasonably practicable;
+
+ b. indicate if You modified the Licensed Material and
+ retain an indication of any previous modifications; and
+
+ c. indicate the Licensed Material is licensed under this
+ Public License, and include the text of, or the URI or
+ hyperlink to, this Public License.
+
+ 2. You may satisfy the conditions in Section 3(a)(1) in any
+ reasonable manner based on the medium, means, and context in
+ which You Share the Licensed Material. For example, it may be
+ reasonable to satisfy the conditions by providing a URI or
+ hyperlink to a resource that includes the required
+ information.
+
+ 3. If requested by the Licensor, You must remove any of the
+ information required by Section 3(a)(1)(A) to the extent
+ reasonably practicable.
+
+ b. ShareAlike.
+
+ In addition to the conditions in Section 3(a), if You Share
+ Adapted Material You produce, the following conditions also apply.
+
+ 1. The Adapter's License You apply must be a Creative Commons
+ license with the same License Elements, this version or
+ later, or a BY-SA Compatible License.
+
+ 2. You must include the text of, or the URI or hyperlink to, the
+ Adapter's License You apply. You may satisfy this condition
+ in any reasonable manner based on the medium, means, and
+ context in which You Share Adapted Material.
+
+ 3. You may not offer or impose any additional or different terms
+ or conditions on, or apply any Effective Technological
+ Measures to, Adapted Material that restrict exercise of the
+ rights granted under the Adapter's License You apply.
+
+
+Section 4 -- Sui Generis Database Rights.
+
+Where the Licensed Rights include Sui Generis Database Rights that
+apply to Your use of the Licensed Material:
+
+ a. for the avoidance of doubt, Section 2(a)(1) grants You the right
+ to extract, reuse, reproduce, and Share all or a substantial
+ portion of the contents of the database;
+
+ b. if You include all or a substantial portion of the database
+ contents in a database in which You have Sui Generis Database
+ Rights, then the database in which You have Sui Generis Database
+ Rights (but not its individual contents) is Adapted Material,
+
+ including for purposes of Section 3(b); and
+ c. You must comply with the conditions in Section 3(a) if You Share
+ all or a substantial portion of the contents of the database.
+
+For the avoidance of doubt, this Section 4 supplements and does not
+replace Your obligations under this Public License where the Licensed
+Rights include other Copyright and Similar Rights.
+
+
+Section 5 -- Disclaimer of Warranties and Limitation of Liability.
+
+ a. UNLESS OTHERWISE SEPARATELY UNDERTAKEN BY THE LICENSOR, TO THE
+ EXTENT POSSIBLE, THE LICENSOR OFFERS THE LICENSED MATERIAL AS-IS
+ AND AS-AVAILABLE, AND MAKES NO REPRESENTATIONS OR WARRANTIES OF
+ ANY KIND CONCERNING THE LICENSED MATERIAL, WHETHER EXPRESS,
+ IMPLIED, STATUTORY, OR OTHER. THIS INCLUDES, WITHOUT LIMITATION,
+ WARRANTIES OF TITLE, MERCHANTABILITY, FITNESS FOR A PARTICULAR
+ PURPOSE, NON-INFRINGEMENT, ABSENCE OF LATENT OR OTHER DEFECTS,
+ ACCURACY, OR THE PRESENCE OR ABSENCE OF ERRORS, WHETHER OR NOT
+ KNOWN OR DISCOVERABLE. WHERE DISCLAIMERS OF WARRANTIES ARE NOT
+ ALLOWED IN FULL OR IN PART, THIS DISCLAIMER MAY NOT APPLY TO YOU.
+
+ b. TO THE EXTENT POSSIBLE, IN NO EVENT WILL THE LICENSOR BE LIABLE
+ TO YOU ON ANY LEGAL THEORY (INCLUDING, WITHOUT LIMITATION,
+ NEGLIGENCE) OR OTHERWISE FOR ANY DIRECT, SPECIAL, INDIRECT,
+ INCIDENTAL, CONSEQUENTIAL, PUNITIVE, EXEMPLARY, OR OTHER LOSSES,
+ COSTS, EXPENSES, OR DAMAGES ARISING OUT OF THIS PUBLIC LICENSE OR
+ USE OF THE LICENSED MATERIAL, EVEN IF THE LICENSOR HAS BEEN
+ ADVISED OF THE POSSIBILITY OF SUCH LOSSES, COSTS, EXPENSES, OR
+ DAMAGES. WHERE A LIMITATION OF LIABILITY IS NOT ALLOWED IN FULL OR
+ IN PART, THIS LIMITATION MAY NOT APPLY TO YOU.
+
+ c. The disclaimer of warranties and limitation of liability provided
+ above shall be interpreted in a manner that, to the extent
+ possible, most closely approximates an absolute disclaimer and
+ waiver of all liability.
+
+
+Section 6 -- Term and Termination.
+
+ a. This Public License applies for the term of the Copyright and
+ Similar Rights licensed here. However, if You fail to comply with
+ this Public License, then Your rights under this Public License
+ terminate automatically.
+
+ b. Where Your right to use the Licensed Material has terminated under
+ Section 6(a), it reinstates:
+
+ 1. automatically as of the date the violation is cured, provided
+ it is cured within 30 days of Your discovery of the
+ violation; or
+
+ 2. upon express reinstatement by the Licensor.
+
+ For the avoidance of doubt, this Section 6(b) does not affect any
+ right the Licensor may have to seek remedies for Your violations
+ of this Public License.
+
+ c. For the avoidance of doubt, the Licensor may also offer the
+ Licensed Material under separate terms or conditions or stop
+ distributing the Licensed Material at any time; however, doing so
+ will not terminate this Public License.
+
+ d. Sections 1, 5, 6, 7, and 8 survive termination of this Public
+ License.
+
+
+Section 7 -- Other Terms and Conditions.
+
+ a. The Licensor shall not be bound by any additional or different
+ terms or conditions communicated by You unless expressly agreed.
+
+ b. Any arrangements, understandings, or agreements regarding the
+ Licensed Material not stated herein are separate from and
+ independent of the terms and conditions of this Public License.
+
+
+Section 8 -- Interpretation.
+
+ a. For the avoidance of doubt, this Public License does not, and
+ shall not be interpreted to, reduce, limit, restrict, or impose
+ conditions on any use of the Licensed Material that could lawfully
+ be made without permission under this Public License.
+
+ b. To the extent possible, if any provision of this Public License is
+ deemed unenforceable, it shall be automatically reformed to the
+ minimum extent necessary to make it enforceable. If the provision
+ cannot be reformed, it shall be severed from this Public License
+ without affecting the enforceability of the remaining terms and
+ conditions.
+
+ c. No term or condition of this Public License will be waived and no
+ failure to comply consented to unless expressly agreed to by the
+ Licensor.
+
+ d. Nothing in this Public License constitutes or may be interpreted
+ as a limitation upon, or waiver of, any privileges and immunities
+ that apply to the Licensor or You, including from the legal
+ processes of any jurisdiction or authority.
+
+
+=======================================================================
+
+Creative Commons is not a party to its public
+licenses. Notwithstanding, Creative Commons may elect to apply one of
+its public licenses to material it publishes and in those instances
+will be considered the “Licensor.” The text of the Creative Commons
+public licenses is dedicated to the public domain under the CC0 Public
+Domain Dedication. Except for the limited purpose of indicating that
+material is shared under a Creative Commons public license or as
+otherwise permitted by the Creative Commons policies published at
+creativecommons.org/policies, Creative Commons does not authorize the
+use of the trademark "Creative Commons" or any other trademark or logo
+of Creative Commons without its prior written consent including,
+without limitation, in connection with any unauthorized modifications
+to any of its public licenses or any other arrangements,
+understandings, or agreements concerning use of licensed material. For
+the avoidance of doubt, this paragraph does not form part of the
+public licenses.
+
+Creative Commons may be contacted at creativecommons.org.
=====================================
README
=====================================
@@ -1,13 +1,13 @@
* Copyright
-FFindex was written by Andreas Hauser <andy at splpashground.de>.
+FFindex was written by Andreas Hauser <Andreas.Hauser at LMU.de>.
Please add your name here if you distribute modified versions.
-FFindex is provided under the Create Commons license "Attribution-ShareAlike 3.0",
+FFindex is provided under the Create Commons license "Attribution-ShareAlike 4.0",
which basically captures the spirit of the Gnu Public License (GPL).
See:
-http://creativecommons.org/licenses/by-sa/3.0/
+http://creativecommons.org/licenses/by-sa/4.0/
* Thanks
=====================================
RELEASE_NOTES
=====================================
@@ -1,3 +1,6 @@
+For updated version, please see public git log.
+
+
0.9.9.6
- Fix OS X builds and integrate Makefile.osx
=====================================
VERSION
=====================================
@@ -1 +1 @@
-0.9.9.8
+0.9.9.9
=====================================
rpm/ffindex.spec
=====================================
@@ -1,10 +1,10 @@
Summary: FFindex is a very simple index/database for huge amounts of small files.
Name: ffindex
-Version: 0.9.9.8
+Version: 0.9.9.9
Release: 1
License: Create Commons license "Attribution-ShareAlike 3.0"
Group: Utilities/System
-Source: https://github.com/ahcm/ffindex/archive/0.9.9.8.tar.gz
+Source: https://github.com/ahcm/ffindex/archive/0.9.9.9.tar.gz
%description
FFindex is a very simple index/database for huge amounts of small files. The
files are stored concatenated in one big data file, seperated by '\0'. A second
=====================================
src/Makefile
=====================================
@@ -86,6 +86,9 @@ ffindex_modify: ffindex_modify.o $(FFINDEX_LIBS)
ffindex_unpack: ffindex_unpack.o $(FFINDEX_LIBS)
$(CC) -o $@ ffindex_unpack.o $(LDFLAGS) $(STATIC)
+ffindex_order: ffindex_order.o $(FFINDEX_LIBS)
+ $(CC) -o $@ ffindex_unpack.o $(LDFLAGS) $(STATIC)
+
test:
rm -f /tmp/test.data /tmp/test.ffindex
LD_LIBRARY_PATH=".:$(LD_LIBRARY_PATH)" ./ffindex_build -s /tmp/test.data /tmp/test.ffindex ../test/data ../test/data2
=====================================
src/ffindex.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*/
#define _GNU_SOURCE 1
=====================================
src/ffindex.h
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*
* Ffindex is a very simple database for small files. The files are stored
* concatenated in one big data file, seperated by '\0'. A second file
@@ -21,7 +21,7 @@
#include <stdio.h>
-#define FFINDEX_VERSION 0.998
+#define FFINDEX_VERSION 0.999
#define FFINDEX_COPYRIGHT "\nDesigned and implemented by Andreas Hauser <andy at splashground.de>.\n"
#define FFINDEX_MAX_INDEX_ENTRIES_DEFAULT 80000000
=====================================
src/ffindex_apply_mpi.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* FFindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*
* ffindex_apply
* apply a program to each FFindex entry
@@ -214,8 +214,8 @@ int main(int argn, char **argv)
"\t-d\tFFDATA output file, stdout of program will be captured\n"
"\t-i\tFFINDEX output file, entries get the same name as input entry\n"
FFINDEX_COPYRIGHT,
- argv[0],
- argv[0]);
+ basename(argv[0]),
+ basename(argv[0]));
errno = EINVAL;
goto EXCEPTION;
}
=====================================
src/ffindex_apply_mpi_spawn.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* FFindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*
* ffindex_apply
* apply a program to each FFindex entry
=====================================
src/ffindex_build.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*/
#define _GNU_SOURCE 1
=====================================
src/ffindex_from_fasta.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* FFindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*/
#define _GNU_SOURCE 1
@@ -60,7 +60,7 @@ int main(int argn, char **argv)
version = 1;
break;
default:
- usage(argv[0]);
+ usage(basename(argv[0]));
return EXIT_FAILURE;
}
}
@@ -74,7 +74,7 @@ int main(int argn, char **argv)
if(argn - optind < 3)
{
- usage(argv[0]);
+ usage(basename(argv[0]));
return EXIT_FAILURE;
}
=====================================
src/ffindex_from_tsv.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* FFindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*/
#define _GNU_SOURCE 1
=====================================
src/ffindex_get.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*/
#define _GNU_SOURCE 1
@@ -70,6 +70,7 @@ int main(int argn, char **argv)
ffindex_db->ffdata_filename = data_filename;
ffindex_db->ffindex_filename = index_filename;
ffindex_db->mode[0] = 'r';
+ ffindex_db->num_max_entries = ffcount_lines(index_filename);
ffindex_db = ffindex_index_db_open(ffindex_db);
if(!ffindex_db)
=====================================
src/ffindex_modify.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*/
#define _GNU_SOURCE 1
@@ -71,7 +71,7 @@ int main(int argn, char **argv)
break;
default:
fprintf(stderr, "Option %c not recognized\n", opt);
- usage(argv[0]);
+ usage(basename(argv[0]));
return EXIT_FAILURE;
}
}
=====================================
src/ffindex_optimize.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*/
#define _GNU_SOURCE 1
=====================================
src/ffindex_unpack.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* FFindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*
* ffindex_apply
* apply a program to each FFindex entry
@@ -37,7 +37,7 @@ int main(int argn, char **argv)
fprintf(stderr, "USAGE: %s DATA_FILENAME INDEX_FILENAME OUT_DIR\n"
"\n\tPlease note that a huge number of files might be created!\n"
FFINDEX_COPYRIGHT,
- argv[0]);
+ basename(argv[0]));
return -1;
}
char *data_filename = argv[1];
=====================================
src/ffutil.c
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*
* Ffindex is a very simple database for small files. The files are stored
* concatenated in one big data file, seperated by '\0'. A second file
=====================================
src/ffutil.h
=====================================
@@ -4,10 +4,10 @@
* Please add your name here if you distribute modified versions.
*
* Ffindex is provided under the Create Commons license "Attribution-ShareAlike
- * 3.0", which basically captures the spirit of the Gnu Public License (GPL).
+ * 4.0", which basically captures the spirit of the Gnu Public License (GPL).
*
* See:
- * http://creativecommons.org/licenses/by-sa/3.0/
+ * http://creativecommons.org/licenses/by-sa/4.0/
*
* Ffindex is a very simple database for small files. The files are stored
* concatenated in one big data file, seperated by '\0'. A second file
View it on GitLab: https://salsa.debian.org/med-team/ffindex/commit/4d1c7063e6dafc94067cc3b94f6227e2bde3e7ac
--
View it on GitLab: https://salsa.debian.org/med-team/ffindex/commit/4d1c7063e6dafc94067cc3b94f6227e2bde3e7ac
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20190128/b4022479/attachment-0001.html>
More information about the debian-med-commit
mailing list