Dockerfile

-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 . .
@@ -9,9 +11,12 @@ WORKDIR /opt/hh-suite/build
 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
 
@@ -19,3 +24,4 @@ ENV HHLIB=/usr/local/hh-suite
 ENV PATH="/usr/local/hh-suite/bin:/usr/local/hh-suite/scripts:${PATH}"
 
 CMD ["hhblits"]
+

debian/changelog

-hhsuite (3.1.0-1) UNRELEASED; urgency=medium
+hhsuite (3.2.0-1) unstable; urgency=medium
 
   [ Michael R. Crusoe ]
   * Team upload.
@@ -16,7 +16,7 @@ hhsuite (3.1.0-1) UNRELEASED; urgency=medium
   [ Andrius Merkys ]
   * Revoking executable permission from Perl modules.
 
- -- Andrius Merkys <andrius.merkys@gmail.com>  Sun, 10 Mar 2019 05:55:13 -0400
+ -- Michael R. Crusoe <michael.crusoe@gmail.com>  Tue, 23 Jul 2019 12:06:51 +0200
 
 hhsuite (3.0~beta3+dfsg-3) unstable; urgency=high
 

debian/control

@@ -22,7 +22,7 @@ Depends: ${shlibs:Depends},
          ${perl:Depends},
          ffindex (>= 0.9.9.8),
          hhsuite-data (= ${source:Version}),
-         python
+         python3
 Breaks: hhsuite-data (<= 2.0.16-1)
 Description: sensitive protein sequence searching based on HMM-HMM alignment
  HH-suite is an open-source software package for sensitive protein sequence

debian/copyright

@@ -3,8 +3,8 @@ Upstream-Name: hhsuite
 Upstream-Contact: Andreas Hauser <hauser@genzentrum.lmu.de>
                   Johannes Soeding <soeding@genzentrum.lmu.de>
 Source: ftp://toolkit.lmb.uni-muenchen.de/HH-suite/releases/hhsuite-([0-9.]+)\.tar\.gz
-File-Excluded: scripts/hhpred/
-               lib/ffindex/
+Files-Excluded: scripts/hhpred
+                lib/ffindex
 
 Files: *
 Copyright: 2006, 2012 Johannes Soeding

debian/patches/drop-fmemopen.h.patch

@@ -19,3 +19,25 @@ Author: Sascha Steinbiss <satta@debian.org>
  #include "cs219.lib.h"
  
  #define SWAP(tmp, arg1, arg2) tmp = arg1; arg1 = arg2; arg2 = tmp;
+--- hhsuite.orig/src/cs/cstranslate_app.h
++++ hhsuite/src/cs/cstranslate_app.h
+@@ -32,7 +32,6 @@
+ #include "a3m_compress.h"
+ #include "ffindexdatabase.h"
+ 
+-#include "ext/fmemopen.h"
+ #include "context_data.lib.h"
+ //include "context_data.crf.h"
+ #include "cs219.lib.h"
+--- hhsuite.orig/src/CMakeLists.txt
++++ hhsuite/src/CMakeLists.txt
+@@ -118,9 +118,6 @@
+         hhviterbialgorithm_with_celloff
+         hhviterbialgorithm_and_ss
+         hhviterbialgorithm_with_celloff_and_ss)
+-if (NOT HAVE_FMEMOPEN)
+-target_link_libraries(HH_OBJECTS ext)
+-endif()
+ 
+ add_executable(hhblits hhblits_app.cpp)
+ target_link_libraries(hhblits HH_OBJECTS)

debian/patches/python3

+Author: Michael R. Crusoe <michael.crusoe@gmail.com>
+Description: Scripts are already Python3 compatible; mark them as so
+--- hhsuite.orig/scripts/a3m.py
++++ hhsuite/scripts/a3m.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ 
+ class A3MFormatError(Exception):
+--- hhsuite.orig/scripts/check_a3m.py
++++ hhsuite/scripts/check_a3m.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ from a3m import A3M_Container
+ from a3m import A3MFormatError
+--- hhsuite.orig/scripts/cif2fasta.py
++++ hhsuite/scripts/cif2fasta.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ """
+ Created on Mon Jun 15 21:49:32 2015
+--- hhsuite.orig/scripts/ffindex.py
++++ hhsuite/scripts/ffindex.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ '''
+ Created on Apr 30, 2014
+--- hhsuite.orig/scripts/get_a3m_size.py
++++ hhsuite/scripts/get_a3m_size.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ from a3m import A3M_Container
+ from a3m import A3MFormatError
+--- hhsuite.orig/scripts/hh_reader.py
++++ hhsuite/scripts/hh_reader.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ """
+ Parser for hhr result files created with hhblits|hhsearch|hhalign -o <hhr_file>
+--- hhsuite.orig/scripts/hhmakemodel.py
++++ hhsuite/scripts/hhmakemodel.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ from hh_reader import read_result
+ from copy import deepcopy
+--- hhsuite.orig/scripts/hhsuitedb.py
++++ hhsuite/scripts/hhsuitedb.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ """
+     hhbsuite.py
+--- hhsuite.orig/scripts/pdbfilter.py
++++ hhsuite/scripts/pdbfilter.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/env python3
+ 
+ """
+ Created in Jun 2016

debian/patches/series

@@ -4,3 +4,4 @@ add_Makefile_in_data.patch
 disable-ffindex-build.patch
 drop-fmemopen.h.patch
 disable-AVX-SSE.patch
+python3

lib/ffindex/CMakeLists.txt

-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)
-

lib/ffindex/LICENSE

-## creative commons
-
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lib/ffindex/README.md

-# 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

lib/ffindex/src/CMakeLists.txt

-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)

lib/ffindex/src/ext/CMakeLists.txt

-include(${CMAKE_ROOT}/Modules/CheckFunctionExists.cmake)
-check_function_exists(fmemopen HAVE_FMEMOPEN)
-
-if (NOT HAVE_FMEMOPEN)
-    set(EXT_SRC fmemopen.c fmemopen.h)
-    add_library(ext ${EXT_SRC})
-endif ()

lib/ffindex/src/ext/fmemopen.c

-/**
- * Copyright (c) 2009 Open Information Security Foundation
- *
- * \author Pablo Rincon Crespo <pablo.rincon.crespo@gmail.com>
- *         Based on FMem.c of Alexandre Flori (2008/10/17 AF)
- */
-
-#define _GNU_SOURCE
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
-#include "fmemopen.h"
-
-/**
- * \brief Seek the mem file from offset and whence
- * \param handler pointer to the memfile
- * \param osffset number of bytes to move from whence
- * \param whence SEEK_SET, SEEK_CUR, SEEK_END
- * \retval pos the position by the last operation, -1 if sizes are out of bounds
- */
-static fpos_t SeekFn(void *handler, fpos_t offset, int whence) {
-    size_t pos = 0;
-    fmem_t *mem = handler;
-
-    switch (whence) {
-        case SEEK_SET:
-            if (offset > 0 && (size_t)offset <= mem->size)
-                return mem->pos = offset;
-        break;
-        case SEEK_CUR:
-            if (mem->pos + offset <= mem->size)
-                return mem->pos = offset;
-        break;
-        case SEEK_END:
-            /* must be negative */
-            if (mem->size + offset <= mem->size)
-                return pos = mem->size + offset;
-        break;
-    }
-
-    return -1;
-}
-
-/**
- * \brief Read from the buffer looking for the available memory limits
- * \param handler pointer to the memfile
- * \param buf buffer to read from the handler
- * \param number of bytes to read
- * \retval count , the number of bytes read
- */
-static int ReadFn(void *handler, char *buf, int size) {
-    size_t count = 0;
-    fmem_t *mem = handler;
-    size_t available = mem->size - mem->pos;
-
-    if (size < 0) return - 1;
-
-    if ((size_t)size > available)
-        size = available;
-
-    while (count < (size_t)size)
-        buf[count++] = mem->buffer[mem->pos++];
-
-    return count;
-}
-
-/**
- * \brief Write into the buffer looking for the available memory limits
- * \param handler pointer to the memfile
- * \param buf buffer to write in the handler
- * \param number of bytes to write
- * \retval count , the number of bytes writen
- */
-static int WriteFn(void *handler, const char *buf, int size) {
-    size_t count = 0;
-    fmem_t *mem = handler;
-    size_t available = mem->size - mem->pos;
-
-    if (size < 0) return - 1;
-
-    if ((size_t)size > available)
-        size = available;
-
-    while (count < (size_t)size)
-        mem->buffer[mem->pos++] = buf[count++];
-
-    return count;
-}
-
-/**
- * \brief close the mem file handler
- * \param handler pointer to the memfile
- * \retval 0 on succesful
- */
-static int CloseFn(void *handler) {
-    free (handler);
-    return 0;
-}
-
-/**
- * \brief portable version of SCFmemopen for OS X / BSD built on top of funopen()
- * \param buffer that holds the file content
- * \param size of the file buffer
- * \param mode mode of the file to open
- * \retval pointer to the file; NULL if something is wrong
- */
-FILE *fmemopen(void *buf, size_t size, const char *mode) {
-    fmem_t *mem = (fmem_t *) malloc(sizeof(fmem_t));
-
-    memset(mem, 0, sizeof(fmem_t));
-    mem->size = size, mem->buffer = buf;
-
-    return funopen(mem, ReadFn, WriteFn, SeekFn, CloseFn);
-}

lib/ffindex/src/ext/fmemopen.h

-#ifndef __FMEMOPEN_H__
-#define __FMEMOPEN_H__
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-
-struct fmem {
-    size_t pos;
-    size_t size;
-    char *buffer;
-};
-typedef struct fmem fmem_t;
-
-FILE *fmemopen(void *, size_t, const char *);
-
-#endif /* __FMEMOPEN_H__ */

lib/ffindex/src/ffindex.c

-/*
- * Ffindex
- * written by Andy Hauser <hauser@genzentrum.lmu.de>.
- * Please add your name here if you distribute modified versions.
- *
- * 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/
-*/
-
-#define _GNU_SOURCE 1
-#define _LARGEFILE64_SOURCE 1
-#define _FILE_OFFSET_BITS 64
-
-#include "ffindex.h"
-#include "ffutil.h"
-
-#include <sys/mman.h>
-#include <sys/stat.h>
-#include <sys/types.h>
-#include <dirent.h>
-#include <errno.h>
-#include <limits.h>
-#include <libgen.h>
-#include <search.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <unistd.h>
-
-#include "ext/fmemopen.h" /* For OS not yet implementing this new standard function */
-
-/* XXX Use page size? */
-#define FFINDEX_BUFFER_SIZE 4096
-
-char* ffindex_copyright_text = "Designed and implemented by Andy Hauser <hauser@genzentrum.lmu.de>.";
-
-char* ffindex_copyright()
-{
-  return ffindex_copyright_text;
-}
-
-/* return *out_data_file, *out_index_file, out_offset.
- Setting to a given offset could be supported with a special mode.
- */
-int ffindex_index_open(char *data_filename, char *index_filename, char* mode, FILE **out_data_file, FILE **out_index_file, size_t *out_offset)
-{
-  /* open index and data file, seek to end if needed */
-  if(mode[0] == 'a')
-  {
-    *out_data_file  = fopen(data_filename, "a");
-    if(*out_data_file == NULL) { perror(data_filename); return EXIT_FAILURE; }
-
-    *out_index_file = fopen(index_filename, "a+");
-    if(*out_index_file == NULL) { perror(index_filename); return EXIT_FAILURE; }
-
-    struct stat sb;
-    fstat(fileno(*out_index_file), &sb);
-    fseek(*out_index_file, sb.st_size, SEEK_SET);
-
-    fstat(fileno(*out_data_file), &sb);
-    fseek(*out_data_file, sb.st_size, SEEK_SET);
-    *out_offset = sb.st_size;
-  }
-  else
-  {
-    struct stat st;
-
-    if(stat(data_filename, &st) == 0) { errno = EEXIST; perror(data_filename); return EXIT_FAILURE; }
-    *out_data_file  = fopen(data_filename, "w");
-    if(*out_data_file == NULL) { perror(data_filename); return EXIT_FAILURE; }
-
-    if(stat(index_filename, &st) == 0) { errno = EEXIST; perror(index_filename); return EXIT_FAILURE; }
-    *out_index_file = fopen(index_filename, "w+");
-    if(*out_index_file == NULL) { perror(index_filename); return EXIT_FAILURE; }
-
-    *out_offset = 0;
-  }
-  return EXIT_SUCCESS;
-}
-
-int ffindex_insert_ffindex(FILE* data_file, FILE* index_file, size_t* offset, char* data_to_add, ffindex_index_t* index_to_add)
-{
-  for(size_t entry_i = 0; entry_i < index_to_add->n_entries; entry_i++)
-  {
-    ffindex_entry_t *entry = ffindex_get_entry_by_index(index_to_add, entry_i);
-    if(entry == NULL) { fferror_print(__FILE__, __LINE__, __func__, ""); return EXIT_FAILURE; }
-    int err = ffindex_insert_memory(data_file, index_file, offset, ffindex_get_data_by_entry(data_to_add, entry), entry->length - 1, entry->name); // skip \0 suffix
-    if(err != EXIT_SUCCESS) { fferror_print(__FILE__, __LINE__, __func__, ""); return EXIT_FAILURE;}
-  }
-  return EXIT_SUCCESS;
-}
-
-/* Insert a memory chunk (string even without \0) into ffindex */
-int ffindex_insert_memory(FILE *data_file, FILE *index_file, size_t *offset, char *from_start, size_t from_length, char *name)
-{
-    int myerrno = 0;
-    size_t offset_before = *offset;
-    size_t write_size = fwrite(from_start, sizeof(char), from_length, data_file);
-    *offset += write_size;
-    if(from_length != write_size)
-      fferror_print(__FILE__, __LINE__, __func__, name);
-
-    /* Seperate by '\0' and thus also make sure at least one byte is written */
-    char buffer[1] = {'\0'};
-    if(fwrite(buffer, sizeof(char), 1, data_file) != 1)
-      perror("ffindex_insert_memory");
-    *offset += 1;
-    if(ferror(data_file) != 0)
-      goto EXCEPTION_ffindex_insert_memory;
-
-    /* write index entry */
-    fprintf(index_file, "%s\t%zd\t%zd\n", name, offset_before, *offset - offset_before);
-
-    return myerrno;
-
-EXCEPTION_ffindex_insert_memory:
-    {
-      fferror_print(__FILE__, __LINE__, __func__, "");
-      return myerrno;
-    }
-}
-
-
-/* Insert all file from a list into ffindex */
-int ffindex_insert_list_file(FILE *data_file, FILE *index_file, size_t *start_offset, FILE *list_file)
-{
-  size_t offset = *start_offset;
-  char path[PATH_MAX];
-  while(fgets(path, PATH_MAX, list_file) != NULL)
-    ffindex_insert_file(data_file, index_file, &offset, ffnchomp(path, strlen(path)), basename(path));
-
-  /* update return value */
-  *start_offset = offset;
-  return 0;
-}
-
-
-/* Insert all files from directory into ffindex */
-int ffindex_insert_dir(FILE *data_file, FILE *index_file, size_t *start_offset, char *input_dir_name)
-{
-  DIR *dir = opendir(input_dir_name);
-  if(dir == NULL)
-  {
-    fferror_print(__FILE__, __LINE__, __func__, input_dir_name);
-    return -1;
-  }
-
-  size_t input_dir_name_len = strlen(input_dir_name);
-  char path[PATH_MAX];
-  strncpy(path, input_dir_name, NAME_MAX);
-  if(input_dir_name[input_dir_name_len - 1] != '/')
-  {
-    path[input_dir_name_len] = '/';
-    input_dir_name_len += 1;
-  }
-
-  size_t offset = *start_offset;
-  struct dirent *entry;
-  while((entry = readdir(dir)) != NULL)
-  {
-    if(entry->d_name[0] == '.')
-      continue;
-    strncpy(path + input_dir_name_len, entry->d_name, NAME_MAX);
-    struct stat sb;
-    if(stat(path, &sb) == -1)
-      fferror_print(__FILE__, __LINE__, __func__, path);
-    if(!S_ISREG(sb.st_mode))
-      continue;
-    ffindex_insert_file(data_file, index_file, &offset, path, entry->d_name);
-  }
-  closedir(dir);
-
-  /* update return value */
-  *start_offset = offset;
-
-  return 0;
-}
-
-
-/* Insert one file by path into ffindex */
-int ffindex_insert_file(FILE *data_file, FILE *index_file, size_t *offset, const char *path, char *name)
-{
-    FILE *file = fopen(path, "r");
-    if(file == NULL)
-      return errno;
-
-    int ret = ffindex_insert_filestream(data_file, index_file, offset, file, name);
-    fclose(file);
-    return ret;
-}
-
-/* Insert one file by handle into ffindex */
-int ffindex_insert_filestream(FILE *data_file, FILE *index_file, size_t *offset, FILE* file, char *name)
-{
-    int myerrno = 0;
-    /* copy and paste file to data file */
-    char buffer[FFINDEX_BUFFER_SIZE];
-    size_t offset_before = *offset;
-    size_t read_size;
-    while((read_size = fread(buffer, sizeof(char), sizeof(buffer), file)) > 0)
-    {
-      size_t write_size = fwrite(buffer, sizeof(char), read_size, data_file);
-      *offset += write_size;
-      if(read_size != write_size)
-        fferror_print(__FILE__, __LINE__, __func__, name);
-    }
-    if(ferror(file))
-      warn("fread");
-
-    /* Seperate by '\0' and thus also make sure at least one byte is written */
-    buffer[0] = '\0';
-    if(fwrite(buffer, sizeof(char), 1, data_file) != 1)
-      perror("ffindex_insert_filestream");
-    *offset += 1;
-    if(ferror(data_file) != 0)
-      goto EXCEPTION_ffindex_insert_file;
-
-    /* write index entry */
-    fprintf(index_file, "%s\t%zd\t%zd\n", name, offset_before, *offset - offset_before);
-
-    if(ferror(file) != 0)
-      goto EXCEPTION_ffindex_insert_file;
-
-    return myerrno;
-
-EXCEPTION_ffindex_insert_file:
-    {
-      fferror_print(__FILE__, __LINE__, __func__, "");
-      return myerrno;
-    }
-}
-
-/* XXX not implemented yet */
-int ffindex_restore(FILE *data_file, FILE *index_file, char *input_dir_name)
-{
-  return -1;
-}
-
-
-char* ffindex_mmap_data(FILE *file, size_t* size)
-{
-  struct stat sb;
-  fstat(fileno(file), &sb);
-  *size = sb.st_size;
-  int fd =  fileno(file);
-  if(fd < 0)
-  {
-    fferror_print(__FILE__, __LINE__, __func__, "mmap failed");
-    return MAP_FAILED;
-  }
-  return (char*)mmap(NULL, *size, PROT_READ, MAP_PRIVATE, fd, 0);
-}
-
-
-static int ffindex_compare_entries_by_name(const void *pentry1, const void *pentry2)
-{
-  ffindex_entry_t* entry1 = (ffindex_entry_t*)pentry1;
-  ffindex_entry_t* entry2 = (ffindex_entry_t*)pentry2;
-  return strncmp(entry1->name, entry2->name, FFINDEX_MAX_ENTRY_NAME_LENTH);
-}
-
-ffindex_entry_t* ffindex_get_entry_by_name(ffindex_index_t *index, char *name)
-{
-  if(index != NULL) {
-	return ffindex_bsearch_get_entry(index, name);
-  }
-  else {
-	return NULL;
-  }
-}
-
-ffindex_entry_t* ffindex_bsearch_get_entry(ffindex_index_t *index, char *name)
-{
-  ffindex_entry_t search;
-  strncpy(search.name, name, FFINDEX_MAX_ENTRY_NAME_LENTH);
-  return (ffindex_entry_t*)bsearch(&search, index->entries, index->n_entries, sizeof(ffindex_entry_t), ffindex_compare_entries_by_name);
-}
-
-
-ffindex_index_t* ffindex_index_parse(FILE *index_file, size_t num_max_entries)
-{
-  if(num_max_entries == 0)
-    num_max_entries = FFINDEX_MAX_INDEX_ENTRIES_DEFAULT;
-  size_t nbytes = sizeof(ffindex_index_t) + (sizeof(ffindex_entry_t) * num_max_entries);
-  ffindex_index_t *index = (ffindex_index_t *)malloc(nbytes);
-  if(index == NULL)
-  {
-    fprintf(stderr, "Failed to allocate %ld bytes\n", nbytes);
-    fferror_print(__FILE__, __LINE__, __func__, "malloc failed");
-    return NULL;
-  }
-  index->num_max_entries = num_max_entries;
-
-  index->file = index_file;
-  index->index_data = ffindex_mmap_data(index_file, &(index->index_data_size));
-  if(index->index_data_size == 0)
-    warn("Problem with data file. Is the file empty or is another process reading it?");
-
-  if(index->index_data == MAP_FAILED)
-  {
-    free(index);
-    return NULL;
-  }
-
-  size_t i = 0;
-  char* d = index->index_data;
-  char* end;
-  /* Faster than scanf per line */
-  for(i = 0; d < (index->index_data + index->index_data_size); i++)
-  {
-    int p;
-    for(p = 0; *d != '\t'; d++)
-      index->entries[i].name[p++] = *d;
-    index->entries[i].name[p] = '\0';
-    index->entries[i].offset = strtoull(d, &end, 10);
-    d = end;
-    index->entries[i].length  = strtoull(d, &end, 10);
-    d = end + 1; /* +1 for newline */
-  }
-
-  index->n_entries = i;
-
-  if(index->n_entries == 0)
-    warn("index with 0 entries");
-
-  return index;
-}
-
-ffindex_entry_t* ffindex_get_entry_by_index(ffindex_index_t *index, size_t entry_index)
-{
-  if(index != NULL && entry_index < index->n_entries)
-    return &index->entries[entry_index];
-  else
-    return NULL;
-}
-
-/* Using a function for this looks like overhead. But a more advanced data format,
- * say a compressed one, can do it's magic here.
- */
-char* ffindex_get_data_by_offset(char* data, size_t offset)
-{
-  return data + offset;
-}
-
-
-char* ffindex_get_data_by_entry(char *data, ffindex_entry_t* entry)
-{
-  return ffindex_get_data_by_offset(data, entry->offset);
-}
-
-
-char* ffindex_get_data_by_name(char *data, ffindex_index_t *index, char *name)
-{
-  ffindex_entry_t* entry = ffindex_bsearch_get_entry(index, name);
-
-  if(entry == NULL)
-    return NULL;
-
-  return ffindex_get_data_by_entry(data, entry);
-}
-
-
-char* ffindex_get_data_by_index(char *data, ffindex_index_t *index, size_t entry_index)
-{
-  ffindex_entry_t* entry = ffindex_get_entry_by_index(index, entry_index);
-
-  if(entry == NULL)
-    return NULL;
-
-  return ffindex_get_data_by_entry(data, entry);
-}
-
-
-FILE* ffindex_fopen_by_entry(char *data, ffindex_entry_t* entry)
-{
-  char *filedata = ffindex_get_data_by_offset(data, entry->offset);
-  return fmemopen(filedata, entry->length, "r");
-}
-
-
-FILE* ffindex_fopen_by_name(char *data, ffindex_index_t *index, char *filename)
-{
-  ffindex_entry_t* entry = ffindex_bsearch_get_entry(index, filename);
-
-  if(entry == NULL)
-    return NULL;
-
-  return ffindex_fopen_by_entry(data, entry);
-}
-
-
-void ffindex_sort_index_file(ffindex_index_t *index)
-{
-  qsort(index->entries, index->n_entries, sizeof(ffindex_entry_t), ffindex_compare_entries_by_name);
-}
-
-
-int ffindex_write(ffindex_index_t* index, FILE* index_file)
-{
-  for(size_t i = 0; i < index->n_entries; i++)
-  {
-    ffindex_entry_t ffindex_entry = index->entries[i];
-    if(fprintf(index_file, "%s\t%zd\t%zd\n", ffindex_entry.name, ffindex_entry.offset, ffindex_entry.length) < 0)
-      return EXIT_FAILURE;
-  }
-  return EXIT_SUCCESS;
-}
-
-
-ffindex_index_t* ffindex_unlink_entries(ffindex_index_t* index, char** sorted_names_to_unlink, int n_names)
-{
-  size_t i = index->n_entries - 1;
-  /* walk list of names to delete */
-  for(int n = n_names - 1; n >= 0;  n--)
-  {
-    char* name_to_unlink = sorted_names_to_unlink[n];
-    /* walk index entries */
-    for(; i-- > 0;)
-    {
-      int cmp = strncmp(name_to_unlink, index->entries[i].name, FFINDEX_MAX_ENTRY_NAME_LENTH);
-      if(cmp == 0) /* found entry */
-      {
-        /* Move entries after the unlinked ones to close the gap */
-        size_t n_entries_to_move = index->n_entries - i - 1;
-        if(n_entries_to_move > 0) /* not last element of array */
-          memmove(index->entries + i, index->entries + i + 1, n_entries_to_move * sizeof(ffindex_entry_t));
-        index->n_entries--;
-        break;
-      }
-      else if(cmp > 0) /* not found */
-        break;
-    }
-  }
-
-  return index;
-}
-
-
-ffindex_index_t* ffindex_unlink(ffindex_index_t* index, char* name_to_unlink)
-{
-  ffindex_entry_t* entry = ffindex_bsearch_get_entry(index, name_to_unlink);
-  if(entry == NULL)
-  {
-    fprintf(stderr, "Warning: could not find '%s'\n", name_to_unlink);
-    return index;
-  }
-  /* Move entries after the unlinked one to close the gap */
-  size_t n_entries_to_move = index->entries + index->n_entries - entry - 1;
-  if(n_entries_to_move > 0) /* not last element of array */
-    memmove(entry, entry + 1, n_entries_to_move * sizeof(ffindex_entry_t));
-  index->n_entries--;
-  return index;
-}
-
-void ffsort_index(const char* index_filename) {
-  FILE* index_fh = fopen(index_filename, "r");
-  size_t lines = ffcount_lines(index_filename);
-
-  ffindex_index_t* index = ffindex_index_parse(index_fh, lines);
-  fclose(index_fh);
-
-  if(index == NULL)	{
-    perror("ffindex_index_parse failed");
-    exit(EXIT_FAILURE);
-  }
-
-  ffindex_sort_index_file(index);
-  index_fh = fopen(index_filename, "w");
-  if(index_fh == NULL) { perror(index_filename); }
-  ffindex_write(index, index_fh);
-  fclose(index_fh);
-}
-
-void ffmerge_splits(const char* data_filename, const char* index_filename,
-                    int first_split_index, int last_split_index, int remove_temporary) {
-
-  FILE* data_file  = fopen(data_filename, "w");
-  if( data_file == NULL) {
-    char error_message[2*FILENAME_MAX];
-    sprintf(error_message, "Could not open file: %s", data_filename);
-    perror(error_message);
-    exit(EXIT_FAILURE);
-  }
-
-  FILE* index_file = fopen(index_filename, "w");
-  if(index_file == NULL) {
-    char error_message[2*FILENAME_MAX];
-    sprintf(error_message, "Could not open file: %s", index_filename);
-    perror(error_message);
-    exit(EXIT_FAILURE);
-  }
-
-  size_t offset = 0;
-
-  // Append ffindex split databases
-  for (int i = first_split_index; i <= last_split_index; i++) {
-    char data_file_name_to_add[FILENAME_MAX];
-    char index_file_name_to_add[FILENAME_MAX];
-
-    snprintf(data_file_name_to_add, FILENAME_MAX, "%s.%d", data_filename, i);
-    snprintf(index_file_name_to_add, FILENAME_MAX, "%s.%d", index_filename, i);
-
-    FILE* data_file_to_add = fopen(data_file_name_to_add, "r");
-    if (data_file_to_add == NULL) {
-      char error_message[2*FILENAME_MAX];
-      sprintf(error_message, "Could not open file: %s", data_file_name_to_add);
-      perror(error_message);
-      exit(EXIT_FAILURE);
-    }
-
-    fseek(data_file_to_add, 0L, SEEK_END);
-    size_t size_data_to_add = ftell(data_file_to_add);
-
-    if(size_data_to_add == 0) {
-      fclose(data_file_to_add);
-
-      if(remove_temporary) {
-        remove(data_file_name_to_add);
-        remove(index_file_name_to_add);
-      }
-
-      continue;
-    }
-
-    rewind(data_file_to_add);
-
-    size_t entries = ffcount_lines(index_file_name_to_add);
-    FILE* index_file_to_add = fopen(index_file_name_to_add, "r");
-    if (index_file_to_add == NULL) {
-      char error_message[2*FILENAME_MAX];
-      sprintf(error_message, "Could not open file: %s", index_file_name_to_add);
-      perror(error_message);
-      exit(EXIT_FAILURE);
-    }
-
-    size_t data_size;
-    char *data_to_add = ffindex_mmap_data(data_file_to_add, &data_size);
-    ffindex_index_t* index_to_add = ffindex_index_parse(index_file_to_add, entries);
-
-    for(size_t entry_i = 0; entry_i < index_to_add->n_entries; entry_i++) {
-      ffindex_entry_t *entry = ffindex_get_entry_by_index(index_to_add, entry_i);
-      ffindex_insert_memory(data_file, index_file, &offset,
-                            ffindex_get_data_by_entry(data_to_add, entry),
-                            entry->length - 1, entry->name);
-    }
-
-    fclose(data_file_to_add);
-    fclose(index_file_to_add);
-
-    if(remove_temporary) {
-      remove(data_file_name_to_add);
-      remove(index_file_name_to_add);
-    }
-  }
-
-  fclose(data_file);
-  fclose(index_file);
-
-  ffsort_index(index_filename);
-}
-
-
-/* vim: ts=2 sw=2 et
-*/

lib/ffindex/src/ffindex.h

-/*
- * Ffindex
- * written by Andy Hauser <hauser@genzentrum.lmu.de>.
- * Please add your name here if you distribute modified versions.
- * 
- * 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/
- * 
- * 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
- * contains a plain text index, giving name, offset and length of of the small
- * files.
- */
-
-#ifndef _FFINDEX_H
-
-#define _FFINDEX_H 1
-
-#include <stdio.h>
-
-#define FFINDEX_VERSION 0.980
-#define FFINDEX_MAX_INDEX_ENTRIES_DEFAULT 200000000 
-#define FFINDEX_MAX_ENTRY_NAME_LENTH 32
-
-typedef struct ffindex_entry {
-  size_t offset;
-  size_t length;
-  char name[FFINDEX_MAX_ENTRY_NAME_LENTH];
-} ffindex_entry_t;
-
-typedef struct ffindex_index {
-  char* filename;
-  FILE* file;
-  char* index_data;
-  size_t index_data_size;
-  size_t num_max_entries;
-  size_t n_entries;
-  ffindex_entry_t entries[]; /* This array is as big as the excess memory allocated for this struct. */
-} ffindex_index_t;
-
-/* return *out_data_file, *out_index_file, out_offset. */
-int ffindex_index_open(char *data_filename, char *index_filename, char* mode, FILE **out_data_file, FILE **out_index_file, size_t *out_offset);
-
-int ffindex_insert_filestream(FILE *data_file, FILE *index_file, size_t *offset, FILE* file, char *name);
-
-int ffindex_insert_ffindex(FILE* data_file, FILE* index_file, size_t* offset, char* data_to_add, ffindex_index_t* index_to_add);
-
-ffindex_entry_t* ffindex_get_entry_by_name(ffindex_index_t *index, char *name);
-
-int ffindex_insert_memory(FILE *data_file, FILE *index_file, size_t *offset, char *from_start, size_t from_length, char *name);
-
-int ffindex_insert_file(FILE *data_file, FILE *index_file, size_t *offset, const char *path, char *name);
-
-int ffindex_insert_list_file(FILE *data_file, FILE *index_file, size_t *start_offset, FILE *list_file);
-
-int ffindex_insert_dir(FILE *data_file, FILE *index_file, size_t *offset, char *input_dir_name);
-
-FILE* ffindex_fopen_by_entry(char *data, ffindex_entry_t* entry);
-
-FILE* ffindex_fopen_by_name(char *data, ffindex_index_t *index, char *name);
-
-char* ffindex_mmap_data(FILE *file, size_t* size);
-
-char* ffindex_get_data_by_offset(char* data, size_t offset);
-
-char* ffindex_get_data_by_entry(char *data, ffindex_entry_t* entry);
-
-char* ffindex_get_data_by_name(char *data, ffindex_index_t *index, char *name);
-
-char* ffindex_get_data_by_index(char *data, ffindex_index_t *index, size_t entry_index);
-
-ffindex_entry_t* ffindex_get_entry_by_index(ffindex_index_t *index, size_t entry_index);
-
-ffindex_entry_t* ffindex_get_entry_by_name(ffindex_index_t *index, char *name);
-
-ffindex_index_t* ffindex_index_parse(FILE *index_file, size_t num_max_entries);
-
-ffindex_entry_t* ffindex_bsearch_get_entry(ffindex_index_t *index, char *name);
-
-void ffindex_sort_index_file(ffindex_index_t *index);
-
-int ffindex_write(ffindex_index_t* index, FILE* index_file);
-
-ffindex_index_t* ffindex_unlink(ffindex_index_t* index, char *entry_name);
-
-ffindex_index_t* ffindex_unlink_entries(ffindex_index_t* index, char** sorted_names_to_unlink, int n_names);
-
-int ffindex_insert_filestream(FILE *data_file, FILE *index_file, size_t *offset, FILE* file, char *name);
-
-void ffsort_index(const char* index_filename);
-
-void ffmerge_splits(const char* data_filename, const char* index_filename,
-                    int first_split_index, int last_split_index, int remove_temporary);
-
-char* ffindex_copyright();
-
-#endif

lib/ffindex/src/ffindex_apply_mpi.c

-/* 
- * FFindex
- * written by Andy Hauser <hauser@genzentrum.lmu.de>,
- * and Milot Mirdita <milot@mirdita.de>
- * Please add your name here if you distribute modified versions.
- *
- * 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/
- *
- * ffindex_apply_mpi
- * apply a program to each FFindex entry
- */
-
-#define _GNU_SOURCE 1
-#define _LARGEFILE64_SOURCE 1
-#define _FILE_OFFSET_BITS 64
-
-#include <limits.h> // PIPE_BUF
-#include <stdlib.h> // EXIT_*, system, malloc, free
-#include <unistd.h> // pipe, fork, close, dup2, execvp, write, read, opt*
-#include <stdint.h>
-
-#include <sys/time.h>
-#include <sys/wait.h>
-#include <sys/mman.h> // munmap
-#include <fcntl.h>    // fcntl, F_*, O_*
-#include <signal.h>   // sigaction, sigemptyset
-
-#include <getopt.h>   // getopt_long
-
-#include <spawn.h>     // spawn_*
-
-#include "ffindex.h"
-#include "ffutil.h"
-
-#ifdef HAVE_MPI
-#include "mpq/mpq.h"
-#endif
-
-char read_buffer[400 * 1024 * 1024];
-extern char **environ;
-
-int
-ffindex_apply_by_entry(char *data, ffindex_entry_t *entry, char *program_name, char **program_argv,
-                       FILE *data_file_out, FILE *index_file_out, FILE *log_file_out, size_t *offset, int quiet) {
-    int ret = 0;
-    int capture_stdout = (data_file_out != NULL && index_file_out != NULL);
-
-    int pipefd_stdin[2];
-    int pipefd_stdout[2];
-
-    ret = pipe(pipefd_stdin);
-    if (ret != 0) {
-        fprintf(stderr, "ERROR in pipe stdin!\n");
-        perror(entry->name);
-        return errno;
-    }
-
-    if (capture_stdout) {
-        ret = pipe(pipefd_stdout);
-        if (ret != 0) {
-            fprintf(stderr, "ERROR in pipe stdout!\n");
-            perror(entry->name);
-            return errno;
-        }
-
-        // Flush so child doesn't copy and also flushes, leading to duplicate output
-        fflush(data_file_out);
-        fflush(index_file_out);
-    }
-
-    posix_spawn_file_actions_t factions;
-    posix_spawn_file_actions_init(&factions);
-    posix_spawn_file_actions_addclose(&factions, pipefd_stdin[1]);
-    posix_spawn_file_actions_adddup2(&factions, pipefd_stdin[0], fileno(stdin));
-    if (capture_stdout) {
-        posix_spawn_file_actions_addclose(&factions, pipefd_stdout[0]);
-        posix_spawn_file_actions_adddup2(&factions, pipefd_stdout[1], fileno(stdout));
-    }
-
-    short spawnFlags = 0;
-    posix_spawnattr_t attr;
-    posix_spawnattr_init(&attr);
-#ifdef POSIX_SPAWN_USEVFORK
-    spawnFlags |= POSIX_SPAWN_USEVFORK;
-#endif
-    posix_spawnattr_setflags(&attr, spawnFlags);
-
-    pid_t child_pid;
-
-    struct timeval tv;
-    gettimeofday(&tv, NULL);
-    int64_t start = (tv.tv_sec) * 1000LL + (tv.tv_usec) / 1000;
-    int err = posix_spawnp(&child_pid, program_name, &factions, &attr, program_argv, environ);
-    if (err) {
-        fprintf(stderr, "ERROR in fork()\n");
-        perror(entry->name);
-        return errno;
-    }
-    else {
-        // parent writes to and possible reads from child
-        int flags = 0;
-
-        // Read end is for child only
-        close(pipefd_stdin[0]);
-
-        if (capture_stdout) {
-            close(pipefd_stdout[1]);
-        }
-
-        char *file_data = ffindex_get_data_by_entry(data, entry);
-
-        if (capture_stdout) {
-            flags = fcntl(pipefd_stdout[0], F_GETFL, 0);
-            fcntl(pipefd_stdout[0], F_SETFL, flags | O_NONBLOCK);
-        }
-
-        char *b = read_buffer;
-
-        // Write file data to child's stdin.
-        ssize_t written = 0;
-        // Don't write ffindex trailing '\0'
-        size_t to_write = entry->length - 1;
-        while (written < to_write) {
-            size_t rest = to_write - written;
-            size_t batch_size = PIPE_BUF;
-            if (rest < PIPE_BUF) {
-                batch_size = rest;
-            }
-
-            ssize_t w = write(pipefd_stdin[1], file_data + written, batch_size);
-            if (w < 0 && errno != EPIPE) {
-                fprintf(stderr, "ERROR in child!\n");
-                perror(entry->name);
-                break;
-            }
-            else {
-                written += w;
-            }
-
-            if (capture_stdout) {
-                // To avoid blocking try to read some data
-                ssize_t r = read(pipefd_stdout[0], b, PIPE_BUF);
-                if (r > 0) {
-                    b += r;
-                }
-            }
-        }
-        close(pipefd_stdin[1]); // child gets EOF
-
-        if (capture_stdout) {
-            // Read rest
-            fcntl(pipefd_stdout[0], F_SETFL, flags); // Remove O_NONBLOCK
-            ssize_t r;
-            while ((r = read(pipefd_stdout[0], b, PIPE_BUF)) > 0) {
-                b += r;
-            }
-            close(pipefd_stdout[0]);
-
-            ffindex_insert_memory(data_file_out, index_file_out, offset, read_buffer, b - read_buffer, entry->name);
-        }
-
-        int status;
-        waitpid(child_pid, &status, 0);
-        if (!quiet) {
-            struct timeval tv;
-            gettimeofday(&tv, NULL);
-            int64_t end = (tv.tv_sec) * 1000LL + (tv.tv_usec) / 1000;
-            fprintf(log_file_out, "%s\t%ld\t%ld\t%lld\t%d\n", entry->name, entry->offset, entry->length, end - start, WEXITSTATUS(status));
-        }
-    }
-
-    return EXIT_SUCCESS;
-}
-
-#ifdef HAVE_MPI
-typedef struct ffindex_apply_mpi_data_s ffindex_apply_mpi_data_t;
-struct ffindex_apply_mpi_data_s {
-    void *data;
-    ffindex_index_t *index;
-    FILE *data_file_out;
-    FILE *index_file_out;
-    FILE *log_file_out;
-    char *program_name;
-    char **program_argv;
-    int quiet;
-    size_t offset;
-};
-
-void ffindex_apply_worker_payload(void *pEnv, const size_t start, const size_t end) {
-    ffindex_apply_mpi_data_t *env = (ffindex_apply_mpi_data_t *) pEnv;
-    for (size_t i = start; i < end; i++) {
-        ffindex_entry_t *entry = ffindex_get_entry_by_index(env->index, i);
-        if (entry == NULL) {
-            break;
-        }
-
-        int error = ffindex_apply_by_entry(env->data, entry,
-                                           env->program_name,
-                                           env->program_argv,
-                                           env->data_file_out,
-                                           env->index_file_out,
-                                           env->log_file_out,
-                                           &(env->offset),
-                                           env->quiet);
-        if (error != 0) {
-            perror(entry->name);
-            break;
-        }
-    }
-
-    return;
-}
-
-#endif
-
-void ignore_signal(int signal) {
-    struct sigaction handler;
-    handler.sa_handler = SIG_IGN;
-    sigemptyset(&handler.sa_mask);
-    handler.sa_flags = 0;
-    sigaction(signal, &handler, NULL);
-}
-
-void usage() {
-    fprintf(stderr,
-            "USAGE: ffindex_apply_mpi [-q] [-k] "
-#ifdef HAVE_MPI
-                    "[-p PARTS] [-l LOG_FILENAME_PREFIX] "
-#endif
-                    "[-d DATA_FILENAME_OUT -i INDEX_FILENAME_OUT] DATA_FILENAME INDEX_FILENAME -- PROGRAM [PROGRAM_ARGS]*\n"
-                    "\nDesigned and implemented by Andy Hauser <hauser@genzentrum.lmu.de> and Milot Mirdita <milot@mirdita.de>.\n\n"
-#ifdef HAVE_MPI
-                    "\t[-p PARTS]\t\tSets how many entries one worker processes per job.\n"
-                    "\t[-l LOG_FILE_PREFIX]\tPrefix for filename for the per worker process logfiles.\n"
-#endif
-                    "\t[-q]\t\t\tSilence the logging of every processed entry.\n"
-                    "\t[-k]\t\t\tKeep unmerged ffindex splits.\n"
-                    "\t[-d DATA_FILENAME_OUT]\tFFindex data file where the results will be saved to.\n"
-                    "\t[-i INDEX_FILENAME_OUT]\tFFindex index file where the results will be saved to.\n"
-                    "\tDATA_FILENAME\t\tInput ffindex data file.\n"
-                    "\tINDEX_FILENAME\t\tInput ffindex index file.\n"
-                    "\tPROGRAM [PROGRAM_ARGS]\tProgram to be executed for every ffindex entry.\n"
-    );
-}
-
-int main(int argn, char **argv) {
-    ignore_signal(SIGPIPE);
-
-    int exit_status = EXIT_SUCCESS;
-
-    int quiet = 0;
-    int keepTmp = 0;
-    char *data_filename_out = NULL;
-    char *index_filename_out = NULL;
-
-#ifdef HAVE_MPI
-    size_t parts = 1;
-    char *log_filename = NULL;
-#endif
-
-    static struct option long_options[] =
-            {
-#ifdef HAVE_MPI
-                    {"parts", required_argument, NULL, 'p'},
-                    {"logfile", required_argument, NULL, 'l'},
-#endif
-                    {"data", required_argument, NULL, 'd'},
-                    {"index", required_argument, NULL, 'i'},
-                    {"quiet", no_argument, NULL, 'q'},
-                    {"keep-tmp", no_argument, NULL, 'k'},
-                    {NULL, 0, NULL, 0}
-            };
-
-    int opt;
-    while (1) {
-        int option_index = 0;
-#ifdef HAVE_MPI
-        const char *short_options = "kql:p:d:i:";
-#else
-        const char* short_options = "kqd:i:";
-#endif
-        opt = getopt_long(argn, argv, short_options, long_options, &option_index);
-
-        if (opt == -1)
-            break;
-
-        switch (opt) {
-#ifdef HAVE_MPI
-            case 'p':
-                parts = strtoull(optarg, NULL, 10);
-                break;
-            case 'l':
-                log_filename = optarg;
-                break;
-#endif
-            case 'd':
-                data_filename_out = optarg;
-                break;
-            case 'i':
-                index_filename_out = optarg;
-                break;
-            case 'q':
-                quiet = 1;
-                break;
-            case 'k':
-                keepTmp = 1;
-                break;
-            default:
-                break;
-        }
-    }
-
-    const int remaining_arguments = argn - optind;
-    if (remaining_arguments < 3) {
-        if (remaining_arguments < 2) {
-            fprintf(stderr, "Please specify input data and index file.\n\n");
-        }
-
-        fprintf(stderr, "Please specify a program to execute.\n\n");
-
-        usage();
-
-        return EXIT_FAILURE;
-    }
-
-    if ((!data_filename_out && index_filename_out) || (data_filename_out && !index_filename_out)) {
-        fprintf(stderr, "Please specify both output data and index file.\n\n");
-
-        usage();
-
-        return EXIT_FAILURE;
-    }
-
-    char *data_filename = argv[optind++];
-    FILE *data_file = fopen(data_filename, "r");
-    if (data_file == NULL) {
-        fferror_print(__FILE__, __LINE__, argv[0], data_filename);
-        return EXIT_FAILURE;
-    }
-
-    char *index_filename = argv[optind++];
-    FILE *index_file = fopen(index_filename, "r");
-    if (index_file == NULL) {
-        fferror_print(__FILE__, __LINE__, argv[0], index_filename);
-        exit_status = EXIT_FAILURE;
-        goto cleanup_1;
-    }
-
-    char *program_name = argv[optind];
-    char **program_argv = argv + optind;
-
-    size_t data_size;
-    char *data = ffindex_mmap_data(data_file, &data_size);
-    if (data == MAP_FAILED) {
-        fferror_print(__FILE__, __LINE__, "ffindex_mmap_data", data_filename);
-        exit_status = EXIT_FAILURE;
-        goto cleanup_2;
-    }
-
-    size_t entries = ffcount_lines(index_filename);
-    ffindex_index_t *index = ffindex_index_parse(index_file, entries);
-    if (index == NULL) {
-        fferror_print(__FILE__, __LINE__, "ffindex_index_parse", index_filename);
-        exit_status = EXIT_FAILURE;
-        goto cleanup_3;
-    }
-
-#ifdef HAVE_MPI
-    if (log_filename != NULL && quiet) {
-        fprintf(stderr, "Please specify either quiet (-q) or a logfile (-l).\n\n");
-        usage();
-        exit_status = EXIT_FAILURE;
-        goto cleanup_3;
-    }
-
-    int mpq_status = MPQ_Init(argn, (const char**)argv, index->n_entries);
-    if (mpq_status == MPQ_SUCCESS) {
-        if (MPQ_rank != MPQ_MASTER) {
-            ffindex_apply_mpi_data_t *env = malloc(sizeof(ffindex_apply_mpi_data_t));
-            env->data = data;
-            env->index = index;
-            env->program_name = program_name;
-            env->program_argv = program_argv;
-            env->quiet = quiet;
-            env->offset = 0;
-
-            env->data_file_out = NULL;
-            if (data_filename_out != NULL) {
-                char data_filename_out_rank[FILENAME_MAX];
-                snprintf(data_filename_out_rank, FILENAME_MAX, "%s.%d",
-                         data_filename_out, MPQ_rank);
-
-                env->data_file_out = fopen(data_filename_out_rank, "w+");
-                if (env->data_file_out == NULL) {
-                    fferror_print(__FILE__, __LINE__, "fopen", data_filename_out_rank);
-                    exit_status = EXIT_FAILURE;
-                    goto cleanup_4;
-                }
-            }
-
-            env->index_file_out = NULL;
-            if (index_filename_out != NULL) {
-                char index_filename_out_rank[FILENAME_MAX];
-                snprintf(index_filename_out_rank, FILENAME_MAX, "%s.%d",
-                         index_filename_out, MPQ_rank);
-
-                env->index_file_out = fopen(index_filename_out_rank, "w+");
-                if (env->index_file_out == NULL) {
-                    fferror_print(__FILE__, __LINE__, "fopen", index_filename_out_rank);
-                    exit_status = EXIT_FAILURE;
-                    goto cleanup_5;
-                }
-            }
-
-            env->log_file_out = stdout;
-            if (log_filename != NULL) {
-                char log_filename_out_rank[FILENAME_MAX];
-                snprintf(log_filename_out_rank, FILENAME_MAX, "%s.%d",
-                         log_filename, MPQ_rank);
-
-                env->log_file_out = fopen(log_filename_out_rank, "w+");
-                if (env->log_file_out == NULL) {
-                    fferror_print(__FILE__, __LINE__, "fopen", log_filename_out_rank);
-                    exit_status = EXIT_FAILURE;
-                    goto cleanup_6;
-                }
-            }
-
-            MPQ_Worker(ffindex_apply_worker_payload, env);
-
-            // make sure that all written files are properly flushed and synced
-            // so that ffmerge_splits wont work on stale data
-            if (env->log_file_out) {
-                int fd = fileno(env->log_file_out);
-                fflush(env->log_file_out);
-                fsync(fd);
-                fclose(env->log_file_out);
-            }
-            cleanup_6:
-            if (env->index_file_out) {
-                int fd = fileno(env->index_file_out);
-                fflush(env->index_file_out);
-                fsync(fd);
-                fclose(env->index_file_out);
-            }
-            cleanup_5:
-            if (env->data_file_out) {
-                int fd = fileno(env->data_file_out);
-                fflush(env->data_file_out);
-                fsync(fd);
-                fclose(env->data_file_out);
-            }
-            cleanup_4:
-            free(env);
-
-            MPI_Barrier(MPI_COMM_WORLD);
-        } else {
-            MPQ_Master(parts);
-            MPI_Barrier(MPI_COMM_WORLD);
-
-            int removeTmp = keepTmp == 0;
-            ffmerge_splits(data_filename_out, index_filename_out, 1, MPQ_size - 1, removeTmp);
-        }
-    } else {
-        if (mpq_status == MPQ_ERROR_NO_WORKERS) {
-            fprintf(stderr, "MPQ_Init: Needs at least one worker process.\n");
-            exit_status = EXIT_FAILURE;
-        }
-    }
-#else
-    FILE* data_file_out = NULL;
-    if (data_filename_out != NULL)
-    {
-        char data_filename_out_rank[FILENAME_MAX];
-        snprintf(data_filename_out_rank, FILENAME_MAX, "%s", data_filename_out);
-
-        data_file_out = fopen(data_filename_out_rank, "w+");
-        if (data_file_out == NULL)
-        {
-            fferror_print(__FILE__, __LINE__, "ffindex_apply_worker_payload", data_filename_out);
-            return EXIT_FAILURE;
-        }
-    }
-
-    FILE* index_file_out = NULL;
-    if (index_filename_out != NULL)
-    {
-        char index_filename_out_rank[FILENAME_MAX];
-        snprintf(index_filename_out_rank, FILENAME_MAX, "%s", index_filename_out);
-
-        index_file_out = fopen(index_filename_out_rank, "w+");
-        if (index_file_out == NULL)
-        {
-            fferror_print(__FILE__, __LINE__, "ffindex_apply_worker_payload", index_filename_out);
-            return EXIT_FAILURE;
-        }
-    }
-
-    size_t offset = 0;
-    for (size_t i = 0; i < index->n_entries; i++)
-    {
-        ffindex_entry_t *entry = ffindex_get_entry_by_index(index, i);
-        if (entry == NULL)
-        {
-            exit_status = errno;
-            break;
-        }
-
-        int error = ffindex_apply_by_entry(data, entry,
-                                           program_name, program_argv,
-                                           data_file_out, index_file_out, stdout,
-                                           &offset, quiet);
-        if (error != 0)
-        {
-            perror(entry->name);
-            exit_status = errno;
-            break;
-        }
-    }
-
-    if (index_file_out) {
-        fclose(index_file_out);
-    }
-    if (data_file_out) {
-        fclose(data_file_out);
-    }
-#endif
-
-    munmap(index->index_data, index->index_data_size);
-    free(index);
-
-    cleanup_3:
-    munmap(data, data_size);
-
-    cleanup_2:
-    if (index_file) {
-        fclose(index_file);
-    }
-
-    cleanup_1:
-    if (data_file) {
-        fclose(data_file);
-    }
-
-#ifdef HAVE_MPI
-    MPI_Finalize();
-#endif
-    return exit_status;
-}

lib/ffindex/src/ffindex_build.c

-/*
- * Ffindex
- * written by Andy Hauser <hauser@genzentrum.lmu.de>.
- * Please add your name here if you distribute modified versions.
- * 
- * 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/
-*/
-
-#define _GNU_SOURCE 1
-#define _LARGEFILE64_SOURCE 1
-#define _FILE_OFFSET_BITS 64
-
-#include <unistd.h>
-#include <stdlib.h>
-#include <stdio.h>
-
-#include <sys/types.h>
-#include <sys/stat.h>
-
-#include <getopt.h>
-
-#include "ffindex.h"
-#include "ffutil.h"
-
-#define MAX_FILENAME_LIST_FILES 4096
-
-void usage(char *program_name)
-{
-    fprintf(stderr, "USAGE: %s [-a|-v] [-s] [-f file]* OUT_DATA_FILE OUT_INDEX_FILE [-d 2ND_DATA_FILE -i 2ND_INDEX_FILE] [DIR_TO_INDEX|FILE]*\n"
-                    "\t-a\t\tappend files/indexes, also needed for sorting an already existing ffindex\n"
-                    "\t-d FFDATA_FILE\ta second ffindex data file for inserting/appending\n"
-                    "\t-i FFINDEX_FILE\ta second ffindex index file for inserting/appending\n"
-                    "\t-f FILE\t\tfile containing a list of file names, one per line\n"
-                    "\t\t\t-f can be specified up to %d times\n"
-                    "\t-s\t\tsort index file, so that the index can queried.\n"
-                    "\t\t\tAnother append operations can be done without sorting.\n"
-                    "\t-v\t\tprint version and other info then exit\n"
-                    "\nEXAMPLES:\n"
-                    "\tCreate a new ffindex containing all files from the \"bar/\" directory containing\n"
-                    "\tsay myfile1.txt, myfile2.txt and sort (-s) it so that e.g. ffindex_get can use it.\n"
-                    "\t\t$ ffindex_build -s foo.ffdata foo.ffindex bar/\n"
-                    "\n\tAdd (-a) more files: myfile3.txt, myfile4.txt.\n"
-                    "\t\t$ ffindex_build -a foo.ffdata foo.ffindex myfile3.txt myfile4.txt\n"
-                    "\n\tOops, forgot to sort it (-s) so do it afterwards:\n"
-                    "\t\t$ ffindex_build -as foo.ffdata foo.ffindex\n"
-                    "\nNOTE:\n"
-                    "\tMaximum key/filename length is %d and maximum entries are by default %d\n"
-                    "\tThis can be changed in the sources.\n"
-                    "\nDesigned and implemented by Andreas W. Hauser <hauser@genzentrum.lmu.de>.\n",
-                    program_name, MAX_FILENAME_LIST_FILES, FFINDEX_MAX_ENTRY_NAME_LENTH, FFINDEX_MAX_INDEX_ENTRIES_DEFAULT);
-}
-
-int main(int argn, char** argv)
-{
-  int append = 0, sort = 0, version = 0;
-  int err = EXIT_SUCCESS;
-  char* list_filenames[MAX_FILENAME_LIST_FILES];
-  char* list_ffindex_data[MAX_FILENAME_LIST_FILES];
-  char* list_ffindex_index[MAX_FILENAME_LIST_FILES];
-  size_t list_ffindex_data_index = 0;
-  size_t list_ffindex_index_index = 0;
-  size_t list_filenames_index = 0;
-
-  static struct option long_options[] =
-  {
-    { "append",  no_argument, NULL, 'a' },
-    { "data",    required_argument, NULL, 'd' },
-    { "index",   required_argument, NULL, 'i' },
-    { "file",    required_argument, NULL, 'f' },
-    { "sort",    no_argument, NULL, 's' },
-    { "version", no_argument, NULL, 'v' },
-    { NULL,      0,           NULL,  0  }
-  };
-
-  int opt;
-  while (1)
-  {
-    int option_index = 0;
-    opt = getopt_long(argn, argv, "ad:i:f:sv", long_options, &option_index);
-    if (opt == -1)
-      break;
-
-    switch (opt)
-    {
-      case 'a':
-        append = 1;
-        break;
-      case 'd':
-        list_ffindex_data[list_ffindex_data_index++] = optarg;
-        break;
-      case 'i':
-        list_ffindex_index[list_ffindex_index_index++] = optarg;
-        break;
-      case 'f':
-        list_filenames[list_filenames_index++] = optarg;
-        break;
-      case 's':
-        sort = 1;
-        break;
-      case 'v':
-        version = 1;
-        break;
-      default:
-        usage(argv[0]);
-        return EXIT_FAILURE;
-    }
-  }
-
-  if(version == 1)
-  {
-    /* Don't you dare running it on a platform where byte != 8 bits */
-    printf("%s version %.2f, off_t = %zd bits\n", argv[0], FFINDEX_VERSION, sizeof(off_t) * 8);
-    return EXIT_SUCCESS;
-  }
-
-  if(argn - optind < 2)
-  {
-    usage(argv[0]);
-    return EXIT_FAILURE;
-  }
-
-  if(list_ffindex_data_index != list_ffindex_index_index)
-  {
-    fprintf(stderr, "ERROR: -d and -i must be specified pairwise\n");
-    return EXIT_FAILURE;
-  }
-
-  char *data_filename  = argv[optind++];
-  char *index_filename = argv[optind++];
-  FILE *data_file, *index_file;
-
-  size_t offset = 0;
-
-  /* open index and data file, seek to end if needed */
-  if(append)
-  {
-    data_file  = fopen(data_filename, "a");
-    if( data_file == NULL) { perror(data_filename); return EXIT_FAILURE; }
-
-    index_file = fopen(index_filename, "a+");
-    if(index_file == NULL) { perror(index_filename); return EXIT_FAILURE; }
-
-    struct stat sb;
-    fstat(fileno(data_file), &sb);
-    fseek(data_file, sb.st_size, SEEK_SET);
-    offset = sb.st_size;
-
-    fstat(fileno(index_file), &sb);
-    fseek(index_file, sb.st_size, SEEK_SET);
-  }
-  else
-  {
-    struct stat st;
-
-    if(stat(data_filename, &st) == 0) { errno = EEXIST; perror(data_filename); return EXIT_FAILURE; }
-    data_file  = fopen(data_filename, "w");
-    if( data_file == NULL) { perror(data_filename); return EXIT_FAILURE; }
-
-    if(stat(index_filename, &st) == 0) { errno = EEXIST; perror(index_filename); return EXIT_FAILURE; }
-    index_file = fopen(index_filename, "w+");
-    if(index_file == NULL) { perror(index_filename); return EXIT_FAILURE; }
-  }
-
-
-  /* For each list_file insert */
-  if(list_filenames_index > 0)
-    for(int i = 0; i < list_filenames_index; i++)
-    {
-      FILE *list_file = fopen(list_filenames[i], "r");
-      if( list_file == NULL) { perror(list_filenames[i]); return EXIT_FAILURE; }
-      if(ffindex_insert_list_file(data_file, index_file, &offset, list_file) < 0)
-      {
-        perror(list_filenames[i]);
-        err = -1;
-      }
-    }
-
-  /* Append other ffindexes */
-  if(list_ffindex_data_index > 0)
-  {
-    for(int i = 0; i < list_ffindex_data_index; i++)
-    {
-      FILE* data_file_to_add  = fopen(list_ffindex_data[i], "r");  if(  data_file_to_add == NULL) { perror(list_ffindex_data[i]); return EXIT_FAILURE; }
-      FILE* index_file_to_add = fopen(list_ffindex_index[i], "r"); if( index_file_to_add == NULL) { perror(list_ffindex_index[i]); return EXIT_FAILURE; }
-
-      // ignore empty files
-      struct stat sb;
-      fstat(fileno(data_file_to_add), &sb);
-      if(sb.st_size == 0)
-          continue;
-
-      fstat(fileno(index_file_to_add), &sb);
-      if(sb.st_size == 0)
-          continue;
-
-      size_t data_size;
-      char *data_to_add = ffindex_mmap_data(data_file_to_add, &data_size);
-
-      size_t entries = ffcount_lines(list_ffindex_index[i]);
-      ffindex_index_t* index_to_add = ffindex_index_parse(index_file_to_add, entries);
-      for(size_t entry_i = 0; entry_i < index_to_add->n_entries; entry_i++)
-      {
-        ffindex_entry_t *entry = ffindex_get_entry_by_index(index_to_add, entry_i);
-        ffindex_insert_memory(data_file, index_file, &offset, ffindex_get_data_by_entry(data_to_add, entry), entry->length - 1, entry->name); // skip \0 suffix
-      }
-    }
-  }
-
-
-  /* Insert files and directories into the index */
-  for(int i = optind; i < argn; i++)
-  {
-    char *path = argv[i];
-    struct stat sb;
-    if(stat(path, &sb) == -1)
-    {
-      fferror_print(__FILE__, __LINE__, __func__, path);
-      continue;
-    }
-
-    if(S_ISDIR(sb.st_mode))
-    {
-      err = ffindex_insert_dir(data_file, index_file, &offset, path);
-      if(err < 0)fferror_print(__FILE__, __LINE__, __func__, path);
-    }
-    else if(S_ISREG(sb.st_mode))
-    {
-      ffindex_insert_file(data_file, index_file, &offset, path, path);
-    }
-  }
-  fclose(data_file);
-
-  /* Sort the index entries and write back */
-  if(sort)
-  {
-    fclose(index_file);
-    size_t entries = ffcount_lines(index_filename);
-    index_file = fopen(index_filename, "r+");
-    ffindex_index_t* index = ffindex_index_parse(index_file, entries);
-    if(index == NULL)
-    {
-      fferror_print(__FILE__, __LINE__, __func__, index_filename);
-      exit(EXIT_FAILURE);
-    }
-    fclose(index_file);
-    ffindex_sort_index_file(index);
-    index_file = fopen(index_filename, "w");
-    if(index_file == NULL) { perror(index_filename); return EXIT_FAILURE; }
-    err += ffindex_write(index, index_file);
-  }
-
-  return err;
-}
-
-/* vim: ts=2 sw=2 et
- */

lib/ffindex/src/ffindex_from_fasta.c

-/*
- * FFindex
- * written by Andy Hauser <hauser@genzentrum.lmu.de>.
- * Please add your name here if you distribute modified versions.
- * 
- * 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/
-*/
-
-#define _GNU_SOURCE 1
-#define _LARGEFILE64_SOURCE 1
-#define _FILE_OFFSET_BITS 64
-
-#include <unistd.h>
-#include <stdlib.h>
-#include <stdio.h>
-
-#include <sys/types.h>
-#include <sys/stat.h>
-#include <ctype.h>
-
-#include <getopt.h>
-
-#include "ffindex.h"
-#include "ffutil.h"
-
-#define MAX_FILENAME_LIST_FILES 4096
-#define MAX_ENTRY_LENGTH 100000
-
-
-void usage(char *program_name)
-{
-    fprintf(stderr, "USAGE: %s -v | [-s] data_filename index_filename fasta_filename\n"
-                    "\t-s\tsort index file\n"
-                    "\nBases on a Design and Implementation of Andreas W. Hauser <hauser@genzentrum.lmu.de>.\n", program_name);
-}
-
-int main(int argn, char **argv)
-{
-  int sort = 0, version = 0;
-  int err = EXIT_SUCCESS;
-  static struct option long_options[] =
-  {
-    { "sort",    no_argument, NULL, 's' },
-    { "version", no_argument, NULL, 'v' },
-    { NULL,      0,           NULL,  0  }
-  };
-
-  int opt;
-  while (1)
-  {
-    int option_index = 0;
-    opt = getopt_long(argn, argv, "sv", long_options, &option_index);
-    if (opt == -1)
-      break;
-
-    switch (opt)
-    {
-      case 's':
-        sort = 1;
-        break;
-      case 'v':
-        version = 1;
-        break;
-      default:
-        usage(argv[0]);
-        return EXIT_FAILURE;
-    }
-  }
-
-  if(version == 1)
-  {
-    /* Don't you dare running it on a platform where byte != 8 bits */
-    printf("%s version %.2f, off_t = %zd bits\n", argv[0], FFINDEX_VERSION, sizeof(off_t) * 8);
-    return EXIT_SUCCESS;
-  }
-
-  if(argn - optind < 3)
-  {
-    usage(argv[0]);
-    return EXIT_FAILURE;
-  }
-
-
-  char *data_filename  = argv[optind++];
-  char *index_filename = argv[optind++];
-
-  char *fasta_filename = argv[optind++];
-
-  printf("data file: %s\n", data_filename);
-  printf("index file: %s\n", index_filename);
-  printf("fasta file: %s\n", fasta_filename);
-
-
-  FILE *data_file, *index_file, *fasta_file;
-  size_t offset = 0;
-
-  //open output ffindex
-  struct stat st;
-
-  if(stat(data_filename, &st) == 0) { errno = EEXIST; perror(data_filename); return EXIT_FAILURE; }
-  data_file  = fopen(data_filename, "w");
-  if( data_file == NULL) { perror(data_filename); return EXIT_FAILURE; }
-
-  if(stat(index_filename, &st) == 0) { errno = EEXIST; perror(index_filename); return EXIT_FAILURE; }
-  index_file = fopen(index_filename, "w+");
-  if(index_file == NULL) { perror(index_filename); return EXIT_FAILURE; }
-
-
-  fasta_file = fopen(fasta_filename, "r");
-  if(fasta_file == NULL) { perror(fasta_filename); return EXIT_FAILURE; }
-
-  size_t fasta_size;
-  char *fasta_data = ffindex_mmap_data(fasta_file, &fasta_size);
-//  size_t from_length = 0;
-
-  char name[FFINDEX_MAX_ENTRY_NAME_LENTH];
-  int seq_id = 1;
-  size_t seq_id_length = 0;
-  size_t count_ws = 0;
-
-  char entry[MAX_ENTRY_LENGTH];
-  entry[0] = '>';
-  size_t entry_length = 0;
-
-  for(size_t fasta_offset = 1; fasta_offset < fasta_size; fasta_offset++) // position after first ">"
-  {
-    seq_id_length = 0;
-    count_ws = 0;
-
-    entry_length = 1;
-
-    while(fasta_offset < fasta_size && !(*(fasta_data + fasta_offset) == '>' && *(fasta_data + fasta_offset - 1) == '\n'))
-    {
-      char input = *(fasta_data + fasta_offset);
-
-      //get fasta name
-      if(isspace(input))
-      {
-        count_ws++;
-        name[seq_id_length] = '\0';
-      }
-      else if(count_ws == 0)
-      {
-        name[seq_id_length++] = *(fasta_data + fasta_offset);
-      }
-
-      entry[entry_length++] = input;
-
-      fasta_offset++;
-    }
-
-    if(seq_id_length == 0) {
-      sprintf(name, "%d", seq_id);
-    }
-    seq_id++;
-
-    ffindex_insert_memory(data_file, index_file, &offset, entry, entry_length, name);
-  }
-  fclose(data_file);
-
-  /* Sort the index entries and write back */
-  if(sort)
-  {
-    fclose(index_file);
-
-    size_t entries = ffcount_lines(index_filename);
-    index_file = fopen(index_filename, "r+");
-    ffindex_index_t* index = ffindex_index_parse(index_file, entries);
-    if(index == NULL)
-    {
-      perror("ffindex_index_parse failed");
-      exit(EXIT_FAILURE);
-    }
-    fclose(index_file);
-    ffindex_sort_index_file(index);
-    index_file = fopen(index_filename, "w");
-    if(index_file == NULL) { perror(index_filename); return EXIT_FAILURE; }
-    err += ffindex_write(index, index_file);
-  }
-
-  return err;
-}
-
-/* vim: ts=2 sw=2 et: */

lib/ffindex/src/ffindex_from_fasta_with_split.c

-/*
- * FFindex
- * written by Andy Hauser <hauser@genzentrum.lmu.de>.
- * Please add your name here if you distribute modified versions.
- * 
- * 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/
-*/
-
-#define _GNU_SOURCE 1
-#define _LARGEFILE64_SOURCE 1
-#define _FILE_OFFSET_BITS 64
-
-#include <unistd.h>
-#include <stdlib.h>
-#include <stdio.h>
-
-#include <sys/types.h>
-#include <sys/stat.h>
-#include <unistd.h>
-#include <ctype.h>
-
-
-#include "ffindex.h"
-#include "ffutil.h"
-
-#define MAX_FILENAME_LIST_FILES 4096
-#define MAX_ENTRY_LENGTH 100000
-
-
-void usage(char *program_name)
-{
-    fprintf(stderr, "USAGE: %s -v | [-s] data_header_filename index_header_filename data_sequence_filename index_sequence_filename fasta_filename\n"
-                    "\t-s\tsort index file\n"
-                    "\nBases on a Design and Implementation of Andreas W. Hauser <hauser@genzentrum.lmu.de>.\n", program_name);
-}
-
-void get_short_id(char* id, const char delimiter, const int field) {
-  size_t l = strlen(id);
-  size_t first_separator_index = l;
-  if (field == 1) {
-    first_separator_index = -1;
-  }
-
-  size_t second_separator_index = l;
-
-  int field_counter = 1;
-  for (size_t index = 0; index < l; index++) {
-    if (id[index] == delimiter) {
-      field_counter++;
-      if(field_counter == field && first_separator_index == l) {
-        first_separator_index = index;
-      }
-      else if(field_counter - 1 == field && second_separator_index == l) {
-        second_separator_index = index;
-        break;
-      }
-    }
-  }
-
-  if (field_counter < field) {
-    fprintf(stderr, "Warning: short id could not be extracted from '%s'!", id);
-  }
-
-  char* substr = malloc(sizeof(char*) * (second_separator_index - first_separator_index));
-  strncpy(substr, id + first_separator_index + 1, (second_separator_index - first_separator_index - 1));
-
-  strncpy(id, substr, (second_separator_index - first_separator_index - 1));
-  id[second_separator_index - first_separator_index - 1] = '\0';
-
-  free(substr);
-}
-
-int main(int argn, char **argv)
-{
-  int sort = 0, version = 0;
-  int opt, err = EXIT_SUCCESS;
-  while ((opt = getopt(argn, argv, "sv")) != -1)
-  {
-    switch (opt)
-    {
-      case 's':
-        sort = 1;
-        break;
-      case 'v':
-        version = 1;
-        break;
-      default:
-        usage(argv[0]);
-        return EXIT_FAILURE;
-    }
-  }
-
-  if(version == 1)
-  {
-    /* Don't you dare running it on a platform where byte != 8 bits */
-    printf("%s version %.2f, off_t = %zd bits\n", argv[0], FFINDEX_VERSION, sizeof(off_t) * 8);
-    return EXIT_SUCCESS;
-  }
-
-  if(argn - optind < 3)
-  {
-    usage(argv[0]);
-    return EXIT_FAILURE;
-  }
-
-
-  char *data_header_filename  = argv[optind++];
-  char *index_header_filename = argv[optind++];
-  char *data_sequence_filename = argv[optind++];
-  char *index_sequence_filename = argv[optind++];
-
-  char *fasta_filename = argv[optind++];
-
-  printf("data header file: %s\n", data_header_filename);
-  printf("index header file: %s\n", index_header_filename);
-  printf("data sequence file: %s\n", data_sequence_filename);
-  printf("index sequence file: %s\n", index_sequence_filename);
-  printf("fasta file: %s\n", fasta_filename);
-
-
-  FILE *data_header_file, *index_header_file, *data_sequence_file, *index_sequence_file, *fasta_file;
-  size_t header_offset = 0;
-  size_t sequence_offset = 0;
-
-  struct stat st;
-
-  // open header ffindex
-  if(stat(data_header_filename, &st) == 0) { errno = EEXIST; perror(data_header_filename); return EXIT_FAILURE; }
-  data_header_file  = fopen(data_header_filename, "w");
-  if( data_header_file == NULL) { perror(data_header_filename); return EXIT_FAILURE; }
-
-  if(stat(index_header_filename, &st) == 0) { errno = EEXIST; perror(index_header_filename); return EXIT_FAILURE; }
-  index_header_file = fopen(index_header_filename, "w+");
-  if(index_header_file == NULL) { perror(index_header_filename); return EXIT_FAILURE; }
-
-  //open sequence ffindex
-  if(stat(data_sequence_filename, &st) == 0) { errno = EEXIST; perror(data_sequence_filename); return EXIT_FAILURE; }
-  data_sequence_file  = fopen(data_sequence_filename, "w");
-  if( data_sequence_file == NULL) { perror(data_sequence_filename); return EXIT_FAILURE; }
-
-  if(stat(index_sequence_filename, &st) == 0) { errno = EEXIST; perror(index_sequence_filename); return EXIT_FAILURE; }
-  index_sequence_file = fopen(index_sequence_filename, "w+");
-  if(index_sequence_file == NULL) { perror(index_sequence_filename); return EXIT_FAILURE; }
-
-  fasta_file = fopen(fasta_filename, "r");
-  if(fasta_file == NULL) { perror(fasta_filename); return EXIT_FAILURE; }
-
-  size_t fasta_size;
-  char *fasta_data = ffindex_mmap_data(fasta_file, &fasta_size);
-//  size_t from_length = 0;
-
-  char name[FFINDEX_MAX_ENTRY_NAME_LENTH];
-  int seq_id = 1;
-  size_t seq_id_length = 0;
-  size_t count_ws = 0;
-
-  char header[MAX_ENTRY_LENGTH];
-  header[0] = '>';
-  size_t header_length = 1;
-  char is_header = 1;
-
-  char sequence[MAX_ENTRY_LENGTH];
-  size_t sequence_length = 0;
-
-  for(size_t fasta_offset = 1; fasta_offset < fasta_size; fasta_offset++) // position after first ">"
-  {
-    seq_id_length = 0;
-    count_ws = 0;
-
-    is_header = 1;
-    header_length = 1;
-
-    sequence_length = 0;
-
-    while(fasta_offset < fasta_size && !(*(fasta_data + fasta_offset) == '>' && *(fasta_data + fasta_offset - 1) == '\n'))
-    {
-      char input = *(fasta_data + fasta_offset);
-
-      //get fasta name
-      if(isspace(input))
-      {
-        count_ws++;
-        name[seq_id_length] = '\0';
-      }
-      else if(count_ws == 0)
-      {
-        name[seq_id_length++] = *(fasta_data + fasta_offset);
-      }
-
-      if(input == '\n') {
-        is_header = 0;
-        header[header_length] = '\0';
-        sequence[sequence_length] = '\0';
-      }
-      else {
-        if(is_header == 1) {
-          header[header_length++] = input;
-        }
-        else {
-          sequence[sequence_length++] = input;
-        }
-      }
-
-      fasta_offset++;
-    }
-
-    if(seq_id_length == 0) {
-      sprintf(name, "%d", seq_id);
-    }
-    seq_id++;
-
-    get_short_id(name, '|', 2);
-
-    ffindex_insert_memory(data_header_file, index_header_file, &header_offset, header, header_length, name);
-    ffindex_insert_memory(data_sequence_file, index_sequence_file, &sequence_offset, sequence, sequence_length, name);
-  }
-  fclose(data_header_file);
-  fclose(data_sequence_file);
-
-  fclose(index_header_file);
-  fclose(index_sequence_file);
-
-  /* Sort the index entries and write back */
-  if(sort) {
-    ffsort_index(index_header_filename);
-    ffsort_index(index_sequence_filename);
-  }
-
-  return err;
-}
-
-/* vim: ts=2 sw=2 et: */