New upstream version 3.2.0

FROM alpine:latest as builder

FROM debian:stable-slim as builder

RUN apk add --no-cache gcc g++ cmake musl-dev vim ninja

RUN apt-get update && apt-get install -y \

    build-essential cmake xxd ninja-build \

 && rm -rf /var/lib/apt/lists/*

WORKDIR /opt/hh-suite

ADD . .

RUN cmake -G Ninja -DHAVE_SSE2=1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local/hh-suite ..

RUN ninja && ninja install

FROM alpine:latest

FROM debian:stable-slim

MAINTAINER Milot Mirdita <milot@mirdita.de>

RUN apk add --no-cache libstdc++ libgomp

RUN apt-get update && apt-get install -y \

    libstdc++6 libgomp1 \

 && rm -rf /var/lib/apt/lists/*

COPY --from=builder /usr/local/hh-suite /usr/local/hh-suite

ENV PATH="/usr/local/hh-suite/bin:/usr/local/hh-suite/scripts:${PATH}"

CMD ["hhblits"]

cmake_minimum_required(VERSION 2.8.12 FATAL_ERROR)

SET(HAVE_MPI 1 CACHE BOOL "Have MPI")

project(ffindex C)

include_directories(src)

include_directories(src/ext)

add_subdirectory(src)

## creative commons

# Attribution-ShareAlike 4.0 International

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### Using Creative Commons Public Licenses

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## 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.

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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.

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   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

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   3. __Term.__ The term of this Public License is specified in Section 6(a).

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   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).

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### Section 3 – License Conditions.

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   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);

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         v. a URI or hyperlink to the Licensed Material to the extent reasonably practicable;

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   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.

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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.__

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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](https://creativecommons.org/publicdomain/zero/1.0/legalcode). 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](http://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.

# FFindex - A database wrapped around mmap

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

file contains a plain text index, giving name, offset and length of of the

small files. The lookup is currently done with a binary search on an array made

from the index file. The attatched binaries (see Usage below) and their source

code shall give an impression of how to use the functions supported by the library in C/C++ code.

## Copyright

FFindex was written by Andreas Hauser <hauser@genzentrum.lmu.de>.

Please add your name here if you distribute modified versions.

* Martin Steinegger <martin.steinegger@mpibpc.mpg.de>

* Markus Meier <markus.meier@mpibpc.mpg.de>

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/4.0/

## Thanks

Thanks to Laszlo Kajan for creating and maintaining Debian packages

and many suggestions to improve the build and user experience.

## Installation

### Compilation

With the sourcecode ready, simply run cmake with the default settings and libraries should be auto-detected:

	mkdir build

	cd build

	cmake -DCMAKE_BUILD_TYPE=RelWithDebInfo -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX=${INSTALL_BASE_DIR} ..

	make

	make install

**Please use a sensible value for ${INSTALL_BASE_DIR}, e.g. /usr/local or /opt/ffindex or $HOME/ffindex**

### Setting environment variables

Please note that before querying or unlinking entries a ffindex must be

sorted, although you can add to it without. So either specify -s with

ffindex_build or sorted later with ffindex_modify -s.

Setup environment:

	export PATH="${INSTALL_BASE_DIR}/bin:${PATH}"

	export LD_LIBRARY_PATH="${INSTALL_BASE_DIR}/lib:${LD_LIBRARY_PATH}"

On OS X set DYLD_LIBRARY_PATH instead of LD_LIBRARY_PATH.

## Usage

Build index from files in test/data and test/data2.

	ffindex_build -s /tmp/test.data /tmp/test.ffindex test/data test/data2

Retrieve three entries:

	ffindex_get  /tmp/test.data /tmp/test.ffindex a b foo

Unlink (Remove reference from index) an entry:

	ffindex_modify -u /tmp/test.ffindex b

Retrieve three entries, "b" should now be missing:

	ffindex_get /tmp/test.data /tmp/test.ffindex a b foo

Convert a Fasta file to ffindex, entry names are incerental IDs starting from 1:

	ffindex_from_fasta -s fasta.ffdata fasta.ffindex NC_007779.ffn

Get first entry by name:

	ffindex_get fasta.ffdata fasta.ffindex 1

Get first and third entry by entry index, this a little faster:

	ffindex_get fasta.ffdata fasta.ffindex -n 1 3

Count the characters including header in each entry:

	ffindex_apply fasta.ffdata fasta.ffindex wc -c

Count the number of characters in each sequence, without the header:

	ffindex_apply fasta.ffdata fasta.ffindex perl -ne '$x += length unless(/^>/); END{print "$x\n"}'

Parallel version for counting the characters including header in each entry:

	mpirun -np 4 ffindex_apply_mpi fasta.ffdata fasta.ffindex -- wc -c

Parallel version for counting the characters including header in each entry and

saving the output to a new ffindex:

	mpirun -np 4 ffindex_apply_mpi fasta.ffdata fasta.ffindex -i out-wc.ffindex -o out-wc.ffdata -- wc -c

set(CMAKE_C_FLAGS "-std=c99 ${CMAKE_C_FLAGS}")

add_library(ffindex ffindex.c ffutil.c)

target_include_directories(ffindex PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})

add_subdirectory(ext)

if (NOT HAVE_FMEMOPEN)

    target_link_libraries(ffindex ext)

endif ()

add_executable(ffindex_apply ffindex_apply_mpi.c)

target_link_libraries(ffindex_apply ffindex)

set_property(TARGET ffindex_apply PROPERTY COMPILE_FLAGS "-UHAVE_MPI")

find_package(MPI)

if (MPI_C_FOUND AND HAVE_MPI)

    add_executable(ffindex_apply_mpi ffindex_apply_mpi.c)

    target_link_libraries(ffindex_apply_mpi ffindex)

    add_subdirectory(mpq)

    set_property(TARGET ffindex_apply_mpi PROPERTY COMPILE_FLAGS "-DHAVE_MPI=1 ${MPI_C_COMPILE_FLAGS}")

    set_property(TARGET ffindex_apply_mpi PROPERTY LINK_FLAGS "${MPI_C_LINK_FLAGS}")

    target_include_directories(ffindex_apply_mpi PUBLIC ${MPI_C_INCLUDE_PATH})

    target_link_libraries(ffindex_apply_mpi mpq ${MPI_C_LIBRARIES})

    install(TARGETS ffindex_apply_mpi DESTINATION bin)

endif ()

add_executable(ffindex_reduce ffindex_reduce.c)

target_link_libraries(ffindex_reduce ffindex)

add_executable(ffindex_build ffindex_build.c)

target_link_libraries(ffindex_build ffindex)

add_executable(ffindex_from_fasta ffindex_from_fasta.c)

target_link_libraries(ffindex_from_fasta ffindex)

add_executable(ffindex_get ffindex_get.c)

target_link_libraries(ffindex_get ffindex)

add_executable(ffindex_modify ffindex_modify.c)

target_link_libraries(ffindex_modify ffindex)

add_executable(ffindex_unpack ffindex_unpack.c)

target_link_libraries(ffindex_unpack ffindex)

add_executable(ffindex_order ffindex_order.c)

target_link_libraries(ffindex_order ffindex)

add_executable(ffindex_from_fasta_with_split ffindex_from_fasta_with_split.c)

target_link_libraries(ffindex_from_fasta_with_split ffindex)

INSTALL(TARGETS ffindex_reduce

        ffindex_apply

        ffindex_build

        ffindex_from_fasta

        ffindex_get

        ffindex_modify

        ffindex_unpack

        ffindex_order

        ffindex_from_fasta_with_split

        DESTINATION bin)