[med-svn] [axe-demultiplexer] 01/06: New upstream version 0.3.2+dfsg1
Andreas Tille
tille at debian.org
Sun Dec 4 08:29:14 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository axe-demultiplexer.
commit b53b59239c4dbfec30559f58a65d5652b8b15585
Author: Andreas Tille <tille at debian.org>
Date: Sun Dec 4 09:06:47 2016 +0100
New upstream version 0.3.2+dfsg1
---
src/libqes/.gitignore | 12 -
src/libqes/.gitmodules | 0
src/libqes/.travis.yml | 35 -
src/libqes/AUTHORS | 1 -
src/libqes/CMakeLists.txt | 147 -
src/libqes/LICENSE | 619 ---
src/libqes/README.md | 31 -
src/libqes/TODO.md | 11 -
src/libqes/cmake-modules/CodeCoverage.cmake | 158 -
src/libqes/cmake-modules/FindLIBQES.cmake | 97 -
.../cmake-modules/GetGitRevisionDescription.cmake | 130 -
.../GetGitRevisionDescription.cmake.in | 38 -
src/libqes/cmake-modules/GitSemVer.cmake | 49 -
src/libqes/src/CMakeLists.txt | 27 -
src/libqes/src/crc.c | 101 -
src/libqes/src/crc.h | 46 -
src/libqes/src/qes.h | 42 -
src/libqes/src/qes_compat.c | 82 -
src/libqes/src/qes_compat.h | 45 -
src/libqes/src/qes_config.h.in | 92 -
src/libqes/src/qes_file.c | 520 ---
src/libqes/src/qes_file.h | 229 --
src/libqes/src/qes_libgnu.c | 32 -
src/libqes/src/qes_libgnu.h | 44 -
src/libqes/src/qes_log.c | 267 --
src/libqes/src/qes_log.h | 166 -
src/libqes/src/qes_match.c | 99 -
src/libqes/src/qes_match.h | 66 -
src/libqes/src/qes_seq.c | 232 --
src/libqes/src/qes_seq.h | 219 --
src/libqes/src/qes_seqfile.c | 327 --
src/libqes/src/qes_seqfile.h | 240 --
src/libqes/src/qes_sequtil.c | 272 --
src/libqes/src/qes_sequtil.h | 39 -
src/libqes/src/qes_str.c | 52 -
src/libqes/src/qes_str.h | 184 -
src/libqes/src/qes_util.c | 75 -
src/libqes/src/qes_util.h | 250 --
src/libqes/test/CMakeLists.txt | 45 -
src/libqes/test/benchmarks.c | 311 --
src/libqes/test/data/bad_diff_lens.fastq | 4 -
src/libqes/test/data/bad_nohdr.fastq | 3 -
src/libqes/test/data/bad_noqual.fastq | 3 -
src/libqes/test/data/bad_noqualhdrchr.fastq | 4 -
src/libqes/test/data/bad_noqualhdreol.fastq | 3 -
src/libqes/test/data/empty.fastq | 1 -
src/libqes/test/data/empty.txt | 0
src/libqes/test/data/loremipsum.txt | 11 -
src/libqes/test/data/loremipsum.txt.gz | Bin 427 -> 0 bytes
src/libqes/test/data/nocomment.fasta | 5 -
src/libqes/test/data/random.bin | Bin 8192 -> 0 bytes
src/libqes/test/data/test.fasta | 4061 --------------------
src/libqes/test/data/test.fastq | 4000 -------------------
src/libqes/test/data/test.fastq.bz2 | Bin 17766 -> 0 bytes
src/libqes/test/data/test.fastq.gz | Bin 24811 -> 0 bytes
src/libqes/test/data/test_large.fasta.gz | Bin 317571 -> 0 bytes
src/libqes/test/data/truth/log_test.txt | 2 -
src/libqes/test/data/truth/qes_seq_print.fa | 2 -
src/libqes/test/data/truth/qes_seq_print.fq | 4 -
src/libqes/test/helpers.c | 207 -
src/libqes/test/helpers.h | 56 -
src/libqes/test/kseq.h | 235 --
src/libqes/test/kseqcat.c | 41 -
src/libqes/test/logdemo.c | 50 -
src/libqes/test/qes_seqcat.c | 30 -
src/libqes/test/qes_seqprint.c | 21 -
src/libqes/test/test.c | 80 -
src/libqes/test/test_file.c | 446 ---
src/libqes/test/test_helpers.c | 70 -
src/libqes/test/test_log.c | 189 -
src/libqes/test/test_match.c | 105 -
src/libqes/test/test_seq.c | 500 ---
src/libqes/test/test_seqcats.sh | 34 -
src/libqes/test/test_seqfile.c | 418 --
src/libqes/test/test_sequtil.c | 67 -
src/libqes/test/test_util.c | 161 -
src/libqes/test/testdata.c | 160 -
src/libqes/test/testdata.h | 65 -
src/libqes/test/tests.h | 57 -
src/libqes/test/tinytest/tinytest.c | 493 ---
src/libqes/test/tinytest/tinytest.h | 100 -
src/libqes/test/tinytest/tinytest_macros.h | 199 -
src/libqes/util/make_codon_list.py | 38 -
src/libqes/util/make_codon_map.py | 21 -
84 files changed, 17378 deletions(-)
diff --git a/src/libqes/.gitignore b/src/libqes/.gitignore
deleted file mode 100644
index b383896..0000000
--- a/src/libqes/.gitignore
+++ /dev/null
@@ -1,12 +0,0 @@
-# Editor temp files
-*.swp
-*.bak
-*~
-
-# compiled
-build
-*.o
-*.a
-*.so
-tags
-version
diff --git a/src/libqes/.gitmodules b/src/libqes/.gitmodules
deleted file mode 100644
index e69de29..0000000
diff --git a/src/libqes/.travis.yml b/src/libqes/.travis.yml
deleted file mode 100644
index 89c69e9..0000000
--- a/src/libqes/.travis.yml
+++ /dev/null
@@ -1,35 +0,0 @@
-language: c
-
-sudo: required
-dist: trusty
-
-env:
- - BUILD_TYPE=Release
- - BUILD_TYPE=Debug
- - BUILD_TYPE=Coverage
-
-compiler:
- - clang
- - gcc
-
-notifications:
- email:
- - kdmfoss at gmail.com
-
-install:
- - sudo apt-get install lcov python-pip zlib1g-dev
- - sudo pip install cpp-coveralls
- - mkdir build
- - mkdir target
- - cd build
-
-script:
- - cmake .. -DCMAKE_INSTALL_PREFIX=../target -DCMAKE_BUILD_TYPE=$BUILD_TYPE
- - make
- - ctest --verbose
- - make install
- - test -f ../target/include/qes.h
-
-after_success:
- - cd ..
- - if [ "$BUILD_TYPE" == "Coverage" ] ; then coveralls -e target -e test -e util -e zlib -E '.*\.h' -e build/CMakeFiles; fi
diff --git a/src/libqes/AUTHORS b/src/libqes/AUTHORS
deleted file mode 100644
index cd220fe..0000000
--- a/src/libqes/AUTHORS
+++ /dev/null
@@ -1 +0,0 @@
-Kevin Murray <spam at kdmurray.id.au>
diff --git a/src/libqes/CMakeLists.txt b/src/libqes/CMakeLists.txt
deleted file mode 100644
index 1fb3d6c..0000000
--- a/src/libqes/CMakeLists.txt
+++ /dev/null
@@ -1,147 +0,0 @@
-CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
-PROJECT(libqes C)
-
-# Append cmake-modules to module path
-SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH}
- "${CMAKE_CURRENT_SOURCE_DIR}/cmake-modules")
-
-
-IF (EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/version")
- FILE(STRINGS "${CMAKE_CURRENT_SOURCE_DIR}/version" LIBQES_VERSION)
-ELSE()
- # git describe as versioning
- EXECUTE_PROCESS(COMMAND git describe
- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
- OUTPUT_VARIABLE LIBQES_VERSION
- OUTPUT_STRIP_TRAILING_WHITESPACE)
-ENDIF()
-
-#############################
-## Setup CMAKE Environment ##
-#############################
-
-# Set this before you include libqes as a CMake subproject, so that we know not
-# to add cmake to the install rule
-IF (LIBQES_AS_SUBMODULE)
- SET(LIBQES_DONT_INSTALL True)
-ELSE()
- SET(LIBQES_DONT_INSTALL False)
-ENDIF()
-
-OPTION(NO_OPENMP "Disable OpenMP" False)
-OPTION(NO_ZLIB "Disable zlib" False)
-# Shortcut to enable dev compile options
-OPTION(DEV "Enable developer warnings")
-IF (DEV)
- SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fsanitize=address -fsanitize=leak -fsanitize=undefined")
- SET(CMAKE_BUILD_TYPE Coverage)
-ENDIF()
-
-IF (NOT CMAKE_BUILD_TYPE)
- SET(CMAKE_BUILD_TYPE Release)
-ENDIF()
-
-MESSAGE(STATUS "${CMAKE_BUILD_TYPE} build of ${PROJECT_NAME} version: ${LIBQES_VERSION}")
-
-# Set output directories
-SET(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
-SET(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
-SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
-
-# Include coverage module IFF out build type is Coverage to avoid bailing out
-# with unmet dependencies on Release builds, i.e. other peoples' computers
-IF (CMAKE_BUILD_TYPE STREQUAL "Coverage")
- INCLUDE(CodeCoverage)
-ENDIF()
-
-# Testing
-ENABLE_TESTING()
-
-# Packaging
-SET(CPACK_GENERATOR "TGZ;TBZ2")
-INCLUDE(CPack)
-
-##########################
-## Set Compiler Options ##
-##########################
-
-
-SET(WARN_FLAGS "${WARN_FLAGS} -Wall -Wextra -Wpedantic")
-
-SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=gnu99 -D_GNU_SOURCE ${WARN_FLAGS}")
-
-SET(CMAKE_C_FLAGS_DEBUG "-ggdb")
-SET(CMAKE_C_FLAGS_RELEASE "-O3")
-
-
-###############################
-## Find Packages and Headers ##
-###############################
-
-# Header/symbols
-INCLUDE(CheckSymbolExists)
-INCLUDE(CheckFunctionExists)
-INCLUDE(CheckLibraryExists)
-INCLUDE(CheckIncludeFiles)
-
-CHECK_SYMBOL_EXISTS(vasprintf stdio.h VASPRINTF_FOUND)
-CHECK_SYMBOL_EXISTS(asprintf stdio.h ASPRINTF_FOUND)
-CHECK_SYMBOL_EXISTS(getline stdio.h GETLINE_FOUND)
-CHECK_SYMBOL_EXISTS(strndup string.h STRNDUP_FOUND)
-
-IF (NOT ${NO_ZLIB})
- FIND_PACKAGE(ZLIB 1.2.5 REQUIRED)
- CHECK_LIBRARY_EXISTS(${ZLIB_LIBRARIES} gzbuffer "" GZBUFFER_FOUND)
-ELSE()
- SET(ZLIB_FOUND FALSE)
- SET(GZBUFFER_FOUND FALSE)
- SET(ZLIB_C_FLAGS "")
- SET(ZLIB_LIBRARIES "")
- SET(ZLIB_INCLUDE_DIRS "")
- MESSAGE(STATUS "Building without zlib")
-ENDIF()
-
-IF (NOT ${NO_OPENMP})
- FIND_PACKAGE(OpenMP)
-ELSE()
- SET(OPENMP_FOUND FALSE)
- SET(OpenMP_C_FLAGS "")
- MESSAGE(STATUS "Building without OpenMP")
-ENDIF()
-
-# Set dependency flags appropriately
-SET(LIBQES_DEPENDS_LIBS
- ${LIBQES_DEPENDS_LIBS}
- ${ZLIB_LIBRARIES})
-SET(LIBQES_DEPENDS_INCLUDE_DIRS
- ${LIBQES_DEPENDS_INCLUDE_DIRS}
- ${ZLIB_INCLUDE_DIRS})
-SET(LIBQES_DEPENDS_CFLAGS
- ${LIBQES_DEPENDS_CFLAGS}
- ${ZLIB_CFLAGS}
- ${OpenMP_C_FLAGS})
-
-SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${LIBQES_DEPENDS_CFLAGS}")
-
-
-#####################
-## Set CMake Paths ##
-#####################
-
-# Set include dirs
-INCLUDE_DIRECTORIES(
- ${CMAKE_BINARY_DIR}
- ${CMAKE_CURRENT_SOURCE_DIR}/src
- ${CMAKE_CURRENT_SOURCE_DIR}/test
- ${CMAKE_CURRENT_SOURCE_DIR}/test/tinytest
- ${LIBQES_DEPENDS_INCLUDE_DIRS}
- )
-
-# Set link dirs
-LINK_DIRECTORIES(${CMAKE_BINARY_DIR}/lib)
-
-# Traverse to library source and tests
-ADD_SUBDIRECTORY(src)
-if (NOT LIBQES_AS_SUBMODULE)
- ADD_SUBDIRECTORY(test)
-endif()
diff --git a/src/libqes/LICENSE b/src/libqes/LICENSE
deleted file mode 100644
index bc08fe2..0000000
--- a/src/libqes/LICENSE
+++ /dev/null
@@ -1,619 +0,0 @@
- GNU GENERAL PUBLIC LICENSE
- Version 3, 29 June 2007
-
- Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
- Preamble
-
- The GNU General Public License is a free, copyleft license for
-software and other kinds of works.
-
- The licenses for most software and other practical works are designed
-to take away your freedom to share and change the works. By contrast,
-the GNU General Public License is intended to guarantee your freedom to
-share and change all versions of a program--to make sure it remains free
-software for all its users. We, the Free Software Foundation, use the
-GNU General Public License for most of our software; it applies also to
-any other work released this way by its authors. You can apply it to
-your programs, too.
-
- When we speak of free software, we are referring to freedom, not
-price. Our General Public Licenses are designed to make sure that you
-have the freedom to distribute copies of free software (and charge for
-them if you wish), that you receive source code or can get it if you
-want it, that you can change the software or use pieces of it in new
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-you modify it: responsibilities to respect the freedom of others.
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-GNU General Public License, you may choose any version ever published
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-versions of the GNU General Public License can be used, that proxy's
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-to choose that version for the Program.
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-permissions. However, no additional obligations are imposed on any
-author or copyright holder as a result of your choosing to follow a
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-APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
-HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
-OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
-THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
-IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
-ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
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diff --git a/src/libqes/README.md b/src/libqes/README.md
deleted file mode 100644
index ace5ed8..0000000
--- a/src/libqes/README.md
+++ /dev/null
@@ -1,31 +0,0 @@
-libqes
-======
-
-A C library for various bioinformatics-y tasks. Proper docs will come in time.
-For now, we have reasonable test coverage under `./test/` that demonstrate the
-API.
-
-###Tests:
-
-| Jenkins GNU/Linux | [](http://biojenkins.anu.edu.au/job/libqes/) |
-| ----------------- | --- |
-| Jenkins MinGW | [](http://biojenkins.anu.edu.au/job/libqes-mingw/) |
-| TravisCI | [](https://travis-ci.org/kdmurray91/libqes) |
-| Test Coverage | [](https://coveralls.io/r/kdmurray91/libqes?branch=master) |
-
-
-License
-=======
-
-
-
-All libqes source code is licensed under the GNU Public License version 3, or a
-later version at your preference. For license text, see `./gpl-3.0.txt` or
-[the GNU website here](http://www.gnu.org/licenses/gpl-3.0.html).
-
-The source of `tinytest`, located in `tests/tinytest`, is Copyright 2009-2012
-Nick Matthewson; `tinytest` is distributed under the 3-clause BSD license.
-`tinytest` is hosted at
-[Nick's github page](https://github.com/nmathewson/tinytest).
-
-`src/crc.[ch]` are from gnulib, and are licensed under the LGPL.
diff --git a/src/libqes/TODO.md b/src/libqes/TODO.md
deleted file mode 100644
index 2cc3820..0000000
--- a/src/libqes/TODO.md
+++ /dev/null
@@ -1,11 +0,0 @@
-KDM Todos:
----------
-
-Error handling:
-
- - write tests
-
-qes_seq:
-
- - split qes_seq_print into separate functions for FASTQ and FASTA. Also maybe
- allow line wrapping for FASTA.
diff --git a/src/libqes/cmake-modules/CodeCoverage.cmake b/src/libqes/cmake-modules/CodeCoverage.cmake
deleted file mode 100644
index 749c979..0000000
--- a/src/libqes/cmake-modules/CodeCoverage.cmake
+++ /dev/null
@@ -1,158 +0,0 @@
-#
-# 2012-01-31, Lars Bilke
-# - Enable Code Coverage
-#
-# 2013-09-17, Joakim Söderberg
-# - Added support for Clang.
-# - Some additional usage instructions.
-#
-# USAGE:
-# 1. Copy this file into your cmake modules path.
-#
-# 2. Add the following line to your CMakeLists.txt:
-# INCLUDE(CodeCoverage)
-#
-# 3. Set compiler flags to turn off optimization and enable coverage:
-# SET(CMAKE_CXX_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage")
-# SET(CMAKE_C_FLAGS "-g -O0 -fprofile-arcs -ftest-coverage")
-#
-# 3. Use the function SETUP_TARGET_FOR_COVERAGE to create a custom make target
-# which runs your test executable and produces a lcov code coverage report:
-# Example:
-# SETUP_TARGET_FOR_COVERAGE(
-# my_coverage_target # Name for custom target.
-# test_driver # Name of the test driver executable that runs the tests.
-# # NOTE! This should always have a ZERO as exit code
-# # otherwise the coverage generation will not complete.
-# coverage # Name of output directory.
-# )
-#
-# 4. Build a Debug build:
-# cmake -DCMAKE_BUILD_TYPE=Debug ..
-# make
-# make my_coverage_target
-#
-#
-
-# Check prereqs
-FIND_PROGRAM( GCOV_PATH gcov )
-FIND_PROGRAM( LCOV_PATH lcov )
-FIND_PROGRAM( GENHTML_PATH genhtml )
-FIND_PROGRAM( GCOVR_PATH gcovr PATHS ${CMAKE_SOURCE_DIR}/tests)
-
-
-
-SET(CMAKE_CXX_FLAGS_COVERAGE
- "${CMAKE_CXX_FLAGS_DEBUG} -g -O0 --coverage -fprofile-arcs -ftest-coverage"
- CACHE STRING "Flags used by the C++ compiler during coverage builds."
- FORCE)
-SET(CMAKE_C_FLAGS_COVERAGE
- "${CMAKE_C_FLAGS_DEBUG} -g -O0 --coverage -fprofile-arcs -ftest-coverage"
- CACHE STRING "Flags used by the C compiler during coverage builds."
- FORCE)
-SET(CMAKE_EXE_LINKER_FLAGS_COVERAGE
- ""
- CACHE STRING "Flags used for linking binaries during coverage builds."
- FORCE)
-SET(CMAKE_SHARED_LINKER_FLAGS_COVERAGE
- ""
- CACHE STRING "Flags used by the shared libraries linker during coverage builds."
- FORCE)
-MARK_AS_ADVANCED(
- CMAKE_CXX_FLAGS_COVERAGE
- CMAKE_C_FLAGS_COVERAGE
- CMAKE_EXE_LINKER_FLAGS_COVERAGE
- CMAKE_SHARED_LINKER_FLAGS_COVERAGE )
-
-IF(NOT GCOV_PATH)
- MESSAGE(FATAL_ERROR "gcov not found! Aborting...")
-ENDIF() # NOT GCOV_PATH
-
-IF(NOT CMAKE_COMPILER_IS_GNUCC AND NOT CMAKE_COMPILER_IS_GNUCXX)
- # Clang version 3.0.0 and greater now supports gcov as well.
- MESSAGE(WARNING "Compiler is not GNU gcc! Clang Version 3.0.0 and greater supports gcov as well, but older versions don't.")
-
- IF(NOT "${CMAKE_C_COMPILER_ID}" STREQUAL "Clang" AND NOT "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
- MESSAGE(FATAL_ERROR "Compiler is not GNU gcc! Aborting...")
- ENDIF()
-ENDIF() # NOT CMAKE_COMPILER_IS_GNUCXX
-
-
-
-# Param _targetname The name of new the custom make target
-# Param _testrunner The name of the target which runs the tests.
-# MUST return ZERO always, even on errors.
-# If not, no coverage report will be created!
-# Param _outputname lcov output is generated as _outputname.info
-# HTML report is generated in _outputname/index.html
-# Optional fourth parameter is passed as arguments to _testrunner
-# Pass them in list form, e.g.: "-j;2" for -j 2
-FUNCTION(SETUP_TARGET_FOR_COVERAGE _targetname _testrunner _outputname _coverdir)
-
- IF(NOT LCOV_PATH)
- MESSAGE(FATAL_ERROR "lcov not found! Aborting...")
- ENDIF() # NOT LCOV_PATH
-
- IF(NOT GENHTML_PATH)
- MESSAGE(FATAL_ERROR "genhtml not found! Aborting...")
- ENDIF() # NOT GENHTML_PATH
-
- # Setup target
- ADD_CUSTOM_TARGET(${_targetname}
-
- # Cleanup lcov
- ${LCOV_PATH} --rc lcov_branch_coverage=1 --directory ${_coverdir} --zerocounters
-
- # Run tests
- COMMAND ${_testrunner} ${ARGV4}
-
- # Capturing lcov counters and generating report
- COMMAND ${LCOV_PATH} --rc lcov_branch_coverage=1 --directory ${_coverdir} --capture --output-file ${_outputname}.info
- COMMAND ${GENHTML_PATH} --branch-coverage -o ${_outputname} ${_outputname}.info
- COMMAND ${CMAKE_COMMAND} -E remove ${_outputname}.info
-
- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
- COMMENT "Resetting code coverage counters to zero.\nProcessing code coverage counters and generating report."
- )
-
- # Show info where to find the report
- ADD_CUSTOM_COMMAND(TARGET ${_targetname} POST_BUILD
- COMMAND ;
- COMMENT "Open ./${_outputname}/index.html in your browser to view the coverage report."
- )
-
-ENDFUNCTION() # SETUP_TARGET_FOR_COVERAGE
-
-# Param _targetname The name of new the custom make target
-# Param _testrunner The name of the target which runs the tests
-# Param _outputname cobertura output is generated as _outputname.xml
-# Optional fourth parameter is passed as arguments to _testrunner
-# Pass them in list form, e.g.: "-j;2" for -j 2
-FUNCTION(SETUP_TARGET_FOR_COVERAGE_COBERTURA _targetname _testrunner _outputname)
-
- IF(NOT PYTHON_EXECUTABLE)
- MESSAGE(FATAL_ERROR "Python not found! Aborting...")
- ENDIF() # NOT PYTHON_EXECUTABLE
-
- IF(NOT GCOVR_PATH)
- MESSAGE(FATAL_ERROR "gcovr not found! Aborting...")
- ENDIF() # NOT GCOVR_PATH
-
- ADD_CUSTOM_TARGET(${_targetname}
-
- # Run tests
- ${_testrunner} ${ARGV3}
-
- # Running gcovr
- COMMAND ${GCOVR_PATH} -x -r ${CMAKE_SOURCE_DIR} -e '${CMAKE_SOURCE_DIR}/tests/' -o ${_outputname}.xml
- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
- COMMENT "Running gcovr to produce Cobertura code coverage report."
- )
-
- # Show info where to find the report
- ADD_CUSTOM_COMMAND(TARGET ${_targetname} POST_BUILD
- COMMAND ;
- COMMENT "Cobertura code coverage report saved in ${_outputname}.xml."
- )
-
-ENDFUNCTION() # SETUP_TARGET_FOR_COVERAGE_COBERTURA
diff --git a/src/libqes/cmake-modules/FindLIBQES.cmake b/src/libqes/cmake-modules/FindLIBQES.cmake
deleted file mode 100644
index b62fd79..0000000
--- a/src/libqes/cmake-modules/FindLIBQES.cmake
+++ /dev/null
@@ -1,97 +0,0 @@
-# - Find libqes
-# Find the native libqes includes and library.
-# Once done this will define
-#
-# LIBQES_INCLUDE_DIRS - where to find qes.h, etc.
-# LIBQES_LIBRARIES - List of libraries when using libqes.
-# LIBQES_FOUND - True if libqes found.
-#
-# LIBQES_VERSION_STRING - The version of libqes found (x.y.z)
-# LIBQES_VERSION_MAJOR - The major version of libqes
-# LIBQES_VERSION_MINOR - The minor version of libqes
-# LIBQES_VERSION_PATCH - The patch version of libqes
-# LIBQES_VERSION_PREREL - The pre-release version of libqes
-# LIBQES_VERSION_GIT - The git version of libqes
-#
-# An includer may set LIBQES_ROOT to a libqes installation root to tell
-# this module where to look.
-
-# =============================================================================
-# Copyright 2014 Kevin Murray. Adapted from FindZLIB.cmake
-# Licensed under the 3-clause BSD license
-#
-# Redistribution and use in source and binary forms, with or without
-# modification, are permitted provided that the following conditions
-# are met:
-# 1. Redistributions of source code must retain the above copyright
-# notice, this list of conditions and the following disclaimer.
-# 2. Redistributions in binary form must reproduce the above copyright
-# notice, this list of conditions and the following disclaimer in the
-# documentation and/or other materials provided with the distribution.
-# 3. Neither the name of the University nor the names of its contributors
-# may be used to endorse or promote products derived from this software
-# without specific prior written permission.
-#
-# THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES,
-# INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
-# FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
-# REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
-# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
-# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
-# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
-# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-set(_LIBQES_SEARCHES)
-
-# Search LIBQES_ROOT first if it is set.
-if(LIBQES_ROOT)
- set(_LIBQES_SEARCH_ROOT PATHS ${LIBQES_ROOT} NO_DEFAULT_PATH)
- list(APPEND _LIBQES_SEARCHES _LIBQES_SEARCH_ROOT)
-endif()
-
-# Normal search.
-set(_LIBQES_SEARCH_NORMAL
- PATHS "$ENV{PROGRAMFILES}/libqes"
- )
-list(APPEND _LIBQES_SEARCHES _LIBQES_SEARCH_NORMAL)
-
-# Try each search configuration.
-foreach(search ${_LIBQES_SEARCHES})
- find_path(LIBQES_INCLUDE_DIR NAMES qes.h ${${search}} PATH_SUFFIXES include)
- find_library(LIBQES_LIBRARY NAMES qes ${${search}} PATH_SUFFIXES lib)
-endforeach()
-
-mark_as_advanced(LIBQES_LIBRARY LIBQES_INCLUDE_DIR)
-# Handle version. Again, flogged from zlib
-if(LIBQES_INCLUDE_DIR AND EXISTS "${LIBQES_INCLUDE_DIR}/qes_config.h")
- file(STRINGS "${LIBQES_INCLUDE_DIR}/qes_config.h" LIBQES_H REGEX "^#define LIBQES_VERSION \"[^\"]*\"")
-
- string(REGEX REPLACE "^.*LIBQES_VERSION \"[Vv]?([0-9]+).*$" "\\1" LIBQES_VERSION_MAJOR "${LIBQES_H}")
- string(REGEX REPLACE "^.*LIBQES_VERSION \"[Vv]?[0-9]+\\.([0-9]+).*$" "\\1" LIBQES_VERSION_MINOR "${LIBQES_H}")
- string(REGEX REPLACE "^.*LIBQES_VERSION \"[Vv]?[0-9]+\\.[0-9]+\\.([0-9]+).*$" "\\1" LIBQES_VERSION_PATCH "${LIBQES_H}")
- set(LIBQES_VERSION_STRING "${LIBQES_VERSION_MAJOR}.${LIBQES_VERSION_MINOR}.${LIBQES_VERSION_PATCH}")
-
- # only append a EXTRA version if it exists:
- set(LIBQES_VERSION_EXTRA "")
- if( "${LIBQES_H}" MATCHES "^.*LIBQES_VERSION \"[Vv]?[0-9]+\\.[0-9]+\\.[0-9]+(.+)\\+git.*$")
- set(LIBQES_VERSION_PREREL "${CMAKE_MATCH_1}")
- endif()
- if( "${LIBQES_H}" MATCHES "^.*LIBQES_VERSION \"[Vv]?[0-9]+\\.[0-9]+\\.[0-9]+.*\\+git\\.(.+)$")
- set(LIBQES_VERSION_git "${CMAKE_MATCH_1}")
- endif()
- set(LIBQES_VERSION_STRING "${LIBQES_VERSION_STRING}${LIBQES_VERSION_PREREL}")
-endif()
-
-# handle the QUIETLY and REQUIRED arguments and set LIBQES_FOUND to TRUE if
-# all listed variables are TRUE
-include(FindPackageHandleStandardArgs)
-FIND_PACKAGE_HANDLE_STANDARD_ARGS(LIBQES REQUIRED_VARS LIBQES_LIBRARY LIBQES_INCLUDE_DIR
- VERSION_VAR LIBQES_VERSION_STRING)
-
-if(LIBQES_FOUND)
- set(LIBQES_INCLUDE_DIRS ${LIBQES_INCLUDE_DIR})
- set(LIBQES_LIBRARIES ${LIBQES_LIBRARY})
-endif()
-
diff --git a/src/libqes/cmake-modules/GetGitRevisionDescription.cmake b/src/libqes/cmake-modules/GetGitRevisionDescription.cmake
deleted file mode 100644
index c8d27f2..0000000
--- a/src/libqes/cmake-modules/GetGitRevisionDescription.cmake
+++ /dev/null
@@ -1,130 +0,0 @@
-# - Returns a version string from Git
-#
-# These functions force a re-configure on each git commit so that you can
-# trust the values of the variables in your build system.
-#
-# get_git_head_revision(<refspecvar> <hashvar> [<additional arguments to git describe> ...])
-#
-# Returns the refspec and sha hash of the current head revision
-#
-# git_describe(<var> [<additional arguments to git describe> ...])
-#
-# Returns the results of git describe on the source tree, and adjusting
-# the output so that it tests false if an error occurs.
-#
-# git_get_exact_tag(<var> [<additional arguments to git describe> ...])
-#
-# Returns the results of git describe --exact-match on the source tree,
-# and adjusting the output so that it tests false if there was no exact
-# matching tag.
-#
-# Requires CMake 2.6 or newer (uses the 'function' command)
-#
-# Original Author:
-# 2009-2010 Ryan Pavlik <rpavlik at iastate.edu> <abiryan at ryand.net>
-# http://academic.cleardefinition.com
-# Iowa State University HCI Graduate Program/VRAC
-#
-# Copyright Iowa State University 2009-2010.
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or copy at
-# http://www.boost.org/LICENSE_1_0.txt)
-
-if(__get_git_revision_description)
- return()
-endif()
-set(__get_git_revision_description YES)
-
-# We must run the following at "include" time, not at function call time,
-# to find the path to this module rather than the path to a calling list file
-get_filename_component(_gitdescmoddir ${CMAKE_CURRENT_LIST_FILE} PATH)
-
-function(get_git_head_revision _refspecvar _hashvar)
- set(GIT_PARENT_DIR "${CMAKE_CURRENT_SOURCE_DIR}")
- set(GIT_DIR "${GIT_PARENT_DIR}/.git")
- while(NOT EXISTS "${GIT_DIR}") # .git dir not found, search parent directories
- set(GIT_PREVIOUS_PARENT "${GIT_PARENT_DIR}")
- get_filename_component(GIT_PARENT_DIR ${GIT_PARENT_DIR} PATH)
- if(GIT_PARENT_DIR STREQUAL GIT_PREVIOUS_PARENT)
- # We have reached the root directory, we are not in git
- set(${_refspecvar} "GITDIR-NOTFOUND" PARENT_SCOPE)
- set(${_hashvar} "GITDIR-NOTFOUND" PARENT_SCOPE)
- return()
- endif()
- set(GIT_DIR "${GIT_PARENT_DIR}/.git")
- endwhile()
- # check if this is a submodule
- if(NOT IS_DIRECTORY ${GIT_DIR})
- file(READ ${GIT_DIR} submodule)
- string(REGEX REPLACE "gitdir: (.*)\n$" "\\1" GIT_DIR_RELATIVE ${submodule})
- get_filename_component(SUBMODULE_DIR ${GIT_DIR} PATH)
- get_filename_component(GIT_DIR ${SUBMODULE_DIR}/${GIT_DIR_RELATIVE} ABSOLUTE)
- endif()
- set(GIT_DATA "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/git-data")
- if(NOT EXISTS "${GIT_DATA}")
- file(MAKE_DIRECTORY "${GIT_DATA}")
- endif()
-
- if(NOT EXISTS "${GIT_DIR}/HEAD")
- return()
- endif()
- set(HEAD_FILE "${GIT_DATA}/HEAD")
- configure_file("${GIT_DIR}/HEAD" "${HEAD_FILE}" COPYONLY)
-
- configure_file("${_gitdescmoddir}/GetGitRevisionDescription.cmake.in"
- "${GIT_DATA}/grabRef.cmake"
- @ONLY)
- include("${GIT_DATA}/grabRef.cmake")
-
- set(${_refspecvar} "${HEAD_REF}" PARENT_SCOPE)
- set(${_hashvar} "${HEAD_HASH}" PARENT_SCOPE)
-endfunction()
-
-function(git_describe _var)
- if(NOT GIT_FOUND)
- find_package(Git QUIET)
- endif()
- get_git_head_revision(refspec hash)
- if(NOT GIT_FOUND)
- set(${_var} "GIT-NOTFOUND" PARENT_SCOPE)
- return()
- endif()
- if(NOT hash)
- set(${_var} "HEAD-HASH-NOTFOUND" PARENT_SCOPE)
- return()
- endif()
-
- # TODO sanitize
- #if((${ARGN}" MATCHES "&&") OR
- # (ARGN MATCHES "||") OR
- # (ARGN MATCHES "\\;"))
- # message("Please report the following error to the project!")
- # message(FATAL_ERROR "Looks like someone's doing something nefarious with git_describe! Passed arguments ${ARGN}")
- #endif()
-
- #message(STATUS "Arguments to execute_process: ${ARGN}")
-
- execute_process(COMMAND
- "${GIT_EXECUTABLE}"
- describe
- ${hash}
- ${ARGN}
- WORKING_DIRECTORY
- "${CMAKE_SOURCE_DIR}"
- RESULT_VARIABLE
- res
- OUTPUT_VARIABLE
- out
- ERROR_QUIET
- OUTPUT_STRIP_TRAILING_WHITESPACE)
- if(NOT res EQUAL 0)
- set(out "${out}-${res}-NOTFOUND")
- endif()
-
- set(${_var} "${out}" PARENT_SCOPE)
-endfunction()
-
-function(git_get_exact_tag _var)
- git_describe(out --exact-match ${ARGN})
- set(${_var} "${out}" PARENT_SCOPE)
-endfunction()
diff --git a/src/libqes/cmake-modules/GetGitRevisionDescription.cmake.in b/src/libqes/cmake-modules/GetGitRevisionDescription.cmake.in
deleted file mode 100644
index 888ce13..0000000
--- a/src/libqes/cmake-modules/GetGitRevisionDescription.cmake.in
+++ /dev/null
@@ -1,38 +0,0 @@
-#
-# Internal file for GetGitRevisionDescription.cmake
-#
-# Requires CMake 2.6 or newer (uses the 'function' command)
-#
-# Original Author:
-# 2009-2010 Ryan Pavlik <rpavlik at iastate.edu> <abiryan at ryand.net>
-# http://academic.cleardefinition.com
-# Iowa State University HCI Graduate Program/VRAC
-#
-# Copyright Iowa State University 2009-2010.
-# Distributed under the Boost Software License, Version 1.0.
-# (See accompanying file LICENSE_1_0.txt or copy at
-# http://www.boost.org/LICENSE_1_0.txt)
-
-set(HEAD_HASH)
-
-file(READ "@HEAD_FILE@" HEAD_CONTENTS LIMIT 1024)
-
-string(STRIP "${HEAD_CONTENTS}" HEAD_CONTENTS)
-if(HEAD_CONTENTS MATCHES "ref")
- # named branch
- string(REPLACE "ref: " "" HEAD_REF "${HEAD_CONTENTS}")
- if(EXISTS "@GIT_DIR@/${HEAD_REF}")
- configure_file("@GIT_DIR@/${HEAD_REF}" "@GIT_DATA@/head-ref" COPYONLY)
- elseif(EXISTS "@GIT_DIR@/logs/${HEAD_REF}")
- configure_file("@GIT_DIR@/logs/${HEAD_REF}" "@GIT_DATA@/head-ref" COPYONLY)
- set(HEAD_HASH "${HEAD_REF}")
- endif()
-else()
- # detached HEAD
- configure_file("@GIT_DIR@/HEAD" "@GIT_DATA@/head-ref" COPYONLY)
-endif()
-
-if(NOT HEAD_HASH)
- file(READ "@GIT_DATA@/head-ref" HEAD_HASH LIMIT 1024)
- string(STRIP "${HEAD_HASH}" HEAD_HASH)
-endif()
diff --git a/src/libqes/cmake-modules/GitSemVer.cmake b/src/libqes/cmake-modules/GitSemVer.cmake
deleted file mode 100644
index c112796..0000000
--- a/src/libqes/cmake-modules/GitSemVer.cmake
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright (c) 2014-2015 Kevin Murray <spam at kdmurray.id.au>
-#
-# Permission is hereby granted, free of charge, to any person obtaining
-# a copy of this software and associated documentation files (the
-# "Software"), to deal in the Software without restriction, including
-# without limitation the rights to use, copy, modify, merge, publish,
-# distribute, sublicense, and/or sell copies of the Software, and to
-# permit persons to whom the Software is furnished to do so, subject to
-# the following conditions:
-#
-# The above copyright notice and this permission notice shall be
-# included in all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-# MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
-# BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
-# ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
-# CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-# SOFTWARE.
-
-INCLUDE(GetGitRevisionDescription)
-
-function(GetGitSemVer _var)
- get_git_head_revision(rev hash)
- git_get_exact_tag(tag)
-
- IF(NOT "${tag}" MATCHES "^-")
- SET(vers "${tag}")
- ELSE()
- git_describe(gitdesc "--always")
- if("${gitdesc}" MATCHES "^.+-.+-.+$")
- STRING (REGEX REPLACE "-" " " gdlist ${gitdesc})
- SEPARATE_ARGUMENTS(gdlist)
- LIST(GET gdlist 0 tag)
- LIST(GET gdlist 1 cmts_since_tag)
- SET(vers "${tag}-${cmts_since_tag}-dirty")
- ELSE()
- SET(vers "dirty")
- ENDIF()
- ENDIF()
-
- IF (NOT "${hash}" STREQUAL "")
- STRING(SUBSTRING ${hash} 0 7 hash)
- set(vers "${vers}+git=${hash}")
- ENDIF()
- set(${_var} ${vers} PARENT_SCOPE)
-endfunction()
diff --git a/src/libqes/src/CMakeLists.txt b/src/libqes/src/CMakeLists.txt
deleted file mode 100644
index 5e818d1..0000000
--- a/src/libqes/src/CMakeLists.txt
+++ /dev/null
@@ -1,27 +0,0 @@
-file(GLOB LIBQES_SOURCES qes_*.c)
-
-# Targets
-if(LIBQES_DONT_INSTALL)
- ADD_LIBRARY(qes_static STATIC EXCLUDE_FROM_ALL ${LIBQES_SOURCES})
- ADD_LIBRARY(qes SHARED EXCLUDE_FROM_ALL ${LIBQES_SOURCES})
-else()
- ADD_LIBRARY(qes_static STATIC ${LIBQES_SOURCES})
- ADD_LIBRARY(qes SHARED ${LIBQES_SOURCES})
-endif()
-
-
-SET_TARGET_PROPERTIES(qes_static PROPERTIES OUTPUT_NAME qes)
-TARGET_LINK_LIBRARIES(qes_static ${LIBQES_DEPENDS_LIBS})
-target_include_directories(qes_static PUBLIC ${LIBQES_DEPENDS_INCLUDE_DIRS} ${CMAKE_CURRENT_SOURCE_DIR})
-
-SET_TARGET_PROPERTIES(qes PROPERTIES SONAME_VERSION 0 VERSION 0)
-TARGET_LINK_LIBRARIES(qes ${LIBQES_DEPENDS_LIBS})
-target_include_directories(qes PUBLIC ${LIBQES_DEPENDS_INCLUDE_DIRS} ${CMAKE_CURRENT_SOURCE_DIR})
-
-CONFIGURE_FILE(qes_config.h.in ${CMAKE_BINARY_DIR}/qes_config.h)
-FILE(GLOB LIBQES_HEADERS ${CMAKE_SOURCE_DIR}/src/*.h ${CMAKE_BINARY_DIR}/qes_config.h)
-
-IF (NOT LIBQES_DONT_INSTALL)
- INSTALL(FILES ${LIBQES_HEADERS} DESTINATION "include")
- INSTALL(TARGETS qes qes_static DESTINATION "lib")
-ENDIF()
diff --git a/src/libqes/src/crc.c b/src/libqes/src/crc.c
deleted file mode 100644
index ee4ef56..0000000
--- a/src/libqes/src/crc.c
+++ /dev/null
@@ -1,101 +0,0 @@
-/* crc.c -- cyclic redundancy checks
- Copyright (C) 2005-2006, 2009-2014 Free Software Foundation, Inc.
-
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3, or (at your option)
- any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>. */
-
-/* Written by Simon Josefsson. */
-
-#include "crc.h"
-
-/* Table of CRCs of all 8-bit messages. Generated by running code
- from RFC 1952 modified to print out the table. */
-static const uint32_t crc32_table[256] = {
- 0x00000000, 0x77073096, 0xee0e612c, 0x990951ba, 0x076dc419, 0x706af48f,
- 0xe963a535, 0x9e6495a3, 0x0edb8832, 0x79dcb8a4, 0xe0d5e91e, 0x97d2d988,
- 0x09b64c2b, 0x7eb17cbd, 0xe7b82d07, 0x90bf1d91, 0x1db71064, 0x6ab020f2,
- 0xf3b97148, 0x84be41de, 0x1adad47d, 0x6ddde4eb, 0xf4d4b551, 0x83d385c7,
- 0x136c9856, 0x646ba8c0, 0xfd62f97a, 0x8a65c9ec, 0x14015c4f, 0x63066cd9,
- 0xfa0f3d63, 0x8d080df5, 0x3b6e20c8, 0x4c69105e, 0xd56041e4, 0xa2677172,
- 0x3c03e4d1, 0x4b04d447, 0xd20d85fd, 0xa50ab56b, 0x35b5a8fa, 0x42b2986c,
- 0xdbbbc9d6, 0xacbcf940, 0x32d86ce3, 0x45df5c75, 0xdcd60dcf, 0xabd13d59,
- 0x26d930ac, 0x51de003a, 0xc8d75180, 0xbfd06116, 0x21b4f4b5, 0x56b3c423,
- 0xcfba9599, 0xb8bda50f, 0x2802b89e, 0x5f058808, 0xc60cd9b2, 0xb10be924,
- 0x2f6f7c87, 0x58684c11, 0xc1611dab, 0xb6662d3d, 0x76dc4190, 0x01db7106,
- 0x98d220bc, 0xefd5102a, 0x71b18589, 0x06b6b51f, 0x9fbfe4a5, 0xe8b8d433,
- 0x7807c9a2, 0x0f00f934, 0x9609a88e, 0xe10e9818, 0x7f6a0dbb, 0x086d3d2d,
- 0x91646c97, 0xe6635c01, 0x6b6b51f4, 0x1c6c6162, 0x856530d8, 0xf262004e,
- 0x6c0695ed, 0x1b01a57b, 0x8208f4c1, 0xf50fc457, 0x65b0d9c6, 0x12b7e950,
- 0x8bbeb8ea, 0xfcb9887c, 0x62dd1ddf, 0x15da2d49, 0x8cd37cf3, 0xfbd44c65,
- 0x4db26158, 0x3ab551ce, 0xa3bc0074, 0xd4bb30e2, 0x4adfa541, 0x3dd895d7,
- 0xa4d1c46d, 0xd3d6f4fb, 0x4369e96a, 0x346ed9fc, 0xad678846, 0xda60b8d0,
- 0x44042d73, 0x33031de5, 0xaa0a4c5f, 0xdd0d7cc9, 0x5005713c, 0x270241aa,
- 0xbe0b1010, 0xc90c2086, 0x5768b525, 0x206f85b3, 0xb966d409, 0xce61e49f,
- 0x5edef90e, 0x29d9c998, 0xb0d09822, 0xc7d7a8b4, 0x59b33d17, 0x2eb40d81,
- 0xb7bd5c3b, 0xc0ba6cad, 0xedb88320, 0x9abfb3b6, 0x03b6e20c, 0x74b1d29a,
- 0xead54739, 0x9dd277af, 0x04db2615, 0x73dc1683, 0xe3630b12, 0x94643b84,
- 0x0d6d6a3e, 0x7a6a5aa8, 0xe40ecf0b, 0x9309ff9d, 0x0a00ae27, 0x7d079eb1,
- 0xf00f9344, 0x8708a3d2, 0x1e01f268, 0x6906c2fe, 0xf762575d, 0x806567cb,
- 0x196c3671, 0x6e6b06e7, 0xfed41b76, 0x89d32be0, 0x10da7a5a, 0x67dd4acc,
- 0xf9b9df6f, 0x8ebeeff9, 0x17b7be43, 0x60b08ed5, 0xd6d6a3e8, 0xa1d1937e,
- 0x38d8c2c4, 0x4fdff252, 0xd1bb67f1, 0xa6bc5767, 0x3fb506dd, 0x48b2364b,
- 0xd80d2bda, 0xaf0a1b4c, 0x36034af6, 0x41047a60, 0xdf60efc3, 0xa867df55,
- 0x316e8eef, 0x4669be79, 0xcb61b38c, 0xbc66831a, 0x256fd2a0, 0x5268e236,
- 0xcc0c7795, 0xbb0b4703, 0x220216b9, 0x5505262f, 0xc5ba3bbe, 0xb2bd0b28,
- 0x2bb45a92, 0x5cb36a04, 0xc2d7ffa7, 0xb5d0cf31, 0x2cd99e8b, 0x5bdeae1d,
- 0x9b64c2b0, 0xec63f226, 0x756aa39c, 0x026d930a, 0x9c0906a9, 0xeb0e363f,
- 0x72076785, 0x05005713, 0x95bf4a82, 0xe2b87a14, 0x7bb12bae, 0x0cb61b38,
- 0x92d28e9b, 0xe5d5be0d, 0x7cdcefb7, 0x0bdbdf21, 0x86d3d2d4, 0xf1d4e242,
- 0x68ddb3f8, 0x1fda836e, 0x81be16cd, 0xf6b9265b, 0x6fb077e1, 0x18b74777,
- 0x88085ae6, 0xff0f6a70, 0x66063bca, 0x11010b5c, 0x8f659eff, 0xf862ae69,
- 0x616bffd3, 0x166ccf45, 0xa00ae278, 0xd70dd2ee, 0x4e048354, 0x3903b3c2,
- 0xa7672661, 0xd06016f7, 0x4969474d, 0x3e6e77db, 0xaed16a4a, 0xd9d65adc,
- 0x40df0b66, 0x37d83bf0, 0xa9bcae53, 0xdebb9ec5, 0x47b2cf7f, 0x30b5ffe9,
- 0xbdbdf21c, 0xcabac28a, 0x53b39330, 0x24b4a3a6, 0xbad03605, 0xcdd70693,
- 0x54de5729, 0x23d967bf, 0xb3667a2e, 0xc4614ab8, 0x5d681b02, 0x2a6f2b94,
- 0xb40bbe37, 0xc30c8ea1, 0x5a05df1b, 0x2d02ef8d
-};
-
-/*
- * The following function was extracted from RFC 1952 by Simon
- * Josefsson. It was modified to avoid initial and final XOR, to use
- * size_t for the buffer length, and to use the const keyword.
- */
-uint32_t
-crc32_update_no_xor (uint32_t crc, const char *buf, size_t len)
-{
- size_t n;
-
- for (n = 0; n < len; n++)
- crc = crc32_table[(crc ^ buf[n]) & 0xff] ^ (crc >> 8);
-
- return crc;
-}
-
-uint32_t
-crc32_no_xor (const char *buf, size_t len)
-{
- return crc32_update_no_xor (0L, buf, len);
-}
-
-uint32_t
-crc32_update (uint32_t crc, const char *buf, size_t len)
-{
- return crc32_update_no_xor (crc ^ 0xffffffff, buf, len) ^ 0xffffffff;
-}
-
-uint32_t
-crc32 (const char *buf, size_t len)
-{
- return crc32_update (0L, buf, len);
-}
diff --git a/src/libqes/src/crc.h b/src/libqes/src/crc.h
deleted file mode 100644
index 52c1747..0000000
--- a/src/libqes/src/crc.h
+++ /dev/null
@@ -1,46 +0,0 @@
-/* crc.h -- cyclic redundancy checks
- Copyright (C) 2005, 2009-2014 Free Software Foundation, Inc.
-
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 3 of the License, or
- (at your option) any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>. */
-
-/* Written by Simon Josefsson. */
-
-#ifndef CRC_H
-# define CRC_H 1
-
-#include <stddef.h>
-#include <stdint.h>
-
-/* Compute CRC-32 value of LEN bytes long BUF, and return it. */
-uint32_t crc32 (const char *buf, size_t len);
-
-/* Incrementally update CRC-32 value CRC using LEN bytes long BUF. In
- the first call, use 0 as the value for CRC. Return the updated
- CRC-32 value. */
-uint32_t crc32_update (uint32_t crc, const char *buf, size_t len);
-
-/* Compute modified-CRC-32 value of LEN bytes long BUF, and return it.
- The "modification" is to avoid the initial and final XOR operation.
- Due to historic implementation errors, this variant is sometimes
- used (i.e., in RFC 3961). */
-uint32_t crc32_no_xor (const char *buf, size_t len);
-
-/* Incrementally update modified-CRC-32 value CRC using LEN bytes long
- BUF. In the first call, use 0 as the value for CRC. Return the
- updated modified-CRC-32 value. The "modification" is to avoid the
- initial and final XOR operation. Due to historic implementation
- errors, this variant is sometimes used (i.e., in RFC 3961). */
-uint32_t crc32_update_no_xor (uint32_t crc, const char *buf, size_t len);
-
-#endif /* CRC_H */
diff --git a/src/libqes/src/qes.h b/src/libqes/src/qes.h
deleted file mode 100644
index cb5e27e..0000000
--- a/src/libqes/src/qes.h
+++ /dev/null
@@ -1,42 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ==========================================================================
- *
- * Filename: qes.h
- *
- * Description: Some common sequence analysis stuff
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ===========================================================================
- */
-
-#ifndef LIBQES_H
-#define LIBQES_H
-
-
-/* ##### HEADER FILE INCLUDES ########################################## */
-#include <qes_match.h>
-#include <qes_seqfile.h>
-#include <qes_seq.h>
-#include <qes_sequtil.h>
-#include <qes_str.h>
-#include <qes_util.h>
-#include <qes_file.h>
-
-#endif /* LIBQES_H */
diff --git a/src/libqes/src/qes_compat.c b/src/libqes/src/qes_compat.c
deleted file mode 100644
index 4b6538c..0000000
--- a/src/libqes/src/qes_compat.c
+++ /dev/null
@@ -1,82 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: qes_compat.c
- *
- * Description: Compatibility helpers for cross-platformness
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "qes_compat.h"
-
-
-#ifndef STRNDUP_FOUND
-char *
-strndup(const char *s, size_t n)
-{
- char *dest = malloc(n+1);
- if (dest == NULL) return NULL;
- strncpy(dest, s, n);
- dest[n] = '\0';
- return dest;
-}
-#endif
-
-#ifndef VASPRINTF_FOUND
-int vasprintf(char **ret, const char *format, va_list args)
-{
- va_list copy;
- int count;
- va_copy(copy, args);
-
- *ret = NULL;
-
- count = vsnprintf(NULL, 0, format, args);
- if (count >= 0) {
- char *buffer = malloc(count + 1);
- if (buffer == NULL) {
- count = -1;
- } else if ((count = vsnprintf(buffer, count + 1, format, copy)) < 0) {
- free(buffer);
- }
- else {
- *ret = buffer;
- }
- }
- va_end(copy);
-
- return count;
-}
-#endif
-
-#ifndef ASPRINTF_FOUND
-int asprintf(char **ret, const char *format, ...)
-{
- va_list args;
- int count;
-
- va_start(args, format);
- count = vasprintf(ret, format, args);
- va_end(args);
- return(count);
-}
-#endif
diff --git a/src/libqes/src/qes_compat.h b/src/libqes/src/qes_compat.h
deleted file mode 100644
index b2abdc3..0000000
--- a/src/libqes/src/qes_compat.h
+++ /dev/null
@@ -1,45 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: qes_compat.h
- *
- * Description: Compatibility helpers for cross-platformness
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "qes_config.h"
-#include <stdlib.h>
-#include <stdarg.h>
-#include <stdio.h>
-
-
-#ifndef STRNDUP_FOUND
-char *strndup(const char *s, size_t n);
-#endif
-
-#ifndef VASPRINTF_FOUND
-int vasprintf(char **ret, const char *format, va_list args);
-#endif
-
-#ifndef ASPRINTF_FOUND
-int asprintf(char **ret, const char *format, ...);
-#endif
diff --git a/src/libqes/src/qes_config.h.in b/src/libqes/src/qes_config.h.in
deleted file mode 100644
index a3ae570..0000000
--- a/src/libqes/src/qes_config.h.in
+++ /dev/null
@@ -1,92 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: qes_config.h.in
- *
- * Description: Define various things from CMake.
- *
- * Created: 15/08/14 12:09:59
- * License: GPLv3+
- * Compiler: gcc, clang
- *
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#ifndef QES_CONFIG_H
-#define QES_CONFIG_H
-
-#define LIBQES_VERSION "${LIBQES_VERSION}"
-#cmakedefine GETLINE_FOUND
-#cmakedefine STRNDUP_FOUND
-#cmakedefine ZLIB_FOUND
-#cmakedefine GZBUFFER_FOUND
-#cmakedefine OPENMP_FOUND
-#cmakedefine ASPRINTF_FOUND
-#cmakedefine VASPRINTF_FOUND
-
-/* Definitions to make changing fp type easy */
-#ifdef ZLIB_FOUND
-# include <zlib.h>
-# define QES_ZTYPE gzFile
-# define QES_ZOPEN gzopen
-# define QES_ZDOPEN gzdopen
-# define QES_ZCLOSE gzclose
-# define QES_ZREAD gzread
-# define QES_ZWRITE gzwrite
-# define QES_ZFLUSH(fp) gzflush(fp, Z_SYNC_FLUSH)
-# define QES_ZFPRINTF gzprintf
-# define QES_ZFPUTS gzputs
-# define QES_ZFPUTC gzputc
-# define QES_ZFGETS gzgets
-# define QES_ZFGETC gzgetc
-# define QES_ZFUNGETC gzungetc
-# define QES_ZERR gzerror
-# define QES_ZEOF gzeof
-#ifdef GZBUFFER_FOUND
-# define QES_ZBUFFER gzbuffer
-#endif
-# define QES_ZSEEK gzseek
-# define QES_ZTELL gztell
-# define QES_ZREWIND gzrewind
-#else
-# define QES_ZTYPE FILE*
-# define QES_ZOPEN fopen
-# define QES_ZCLOSE fclose
-# define QES_ZDOPEN fdopen
-# define QES_ZCLOSE fclose
-# define QES_ZREAD(fp, buf, ln) fread(buf, 1, ln, fp)
-# define QES_ZWRITE(fp, buf, ln) fwrite(buf, 1, ln, fp)
-# define QES_ZFLUSH fflush
-# define QES_ZFPRINTF fprintf
-# define QES_ZFPUTS(fp, s) fputs(s, fp)
-# define QES_ZFPUTC(fp, c) fputc(c, fp)
-# define QES_ZFGETS(fp, s, l) fgets(s, l, fp)
-# define QES_ZFGETC fgetc
-# define QES_ZFUNGETC fungetc
-# define QES_ZERR ferror
-# define QES_ZEOF feof
-# define QES_ZBUFFER(fp, sz) setvbuf(fp, NULL, _IOFBF, sz)
-# define QES_ZSEEK fseek
-# define QES_ZTELL ftell
-# define QES_ZREWIND rewind
-#endif
-
-#endif /* QES_CONFIG_H */
diff --git a/src/libqes/src/qes_file.c b/src/libqes/src/qes_file.c
deleted file mode 100644
index 93fee0f..0000000
--- a/src/libqes/src/qes_file.c
+++ /dev/null
@@ -1,520 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: qes_file.c
- *
- * Description: Compressed file IO
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "qes_file.h"
-
-static int
-__qes_file_fill_buffer (struct qes_file *file)
-{
- ssize_t res = 0;
-
- if (!qes_file_ok(file)) {
- return 0;
- }
- if (file->feof || file->eof) {
- file->eof = 1;
- return EOF;
- }
- res = QES_ZREAD(file->fp, file->buffer, QES_FILEBUFFER_LEN - 1);
- if (res < 0) {
- /* Errored */
- return 0;
- } else if (res == 0) {
- /* At both buffer & file EOF */
- file->eof = 1;
- file->feof = 1;
- return EOF;
- } else if (res < (QES_FILEBUFFER_LEN) - 1) {
- /* At file EOF */
- file->feof = 1;
- }
- file->bufiter = file->buffer;
- file->bufend = file->buffer + res;
- file->bufend[0] = '\0';
- return 1;
-}
-
-struct qes_file *
-qes_file_open_ (const char *path, const char *mode, qes_errhandler_func onerr,
- const char *file, int line)
-{
- struct qes_file *qf = NULL;
-
- /* Error out with NULL */
- if (path == NULL || mode == NULL || onerr == NULL || file == NULL) {
- return NULL;
- }
-
- /* create file struct */
- qf = qes_calloc(1, sizeof(*qf));
- /* Open file, handling any errors */
- if (strcmp(path, "-") == 0) {
- if (tolower(mode[0]) == 'r') {
- qf->fp = QES_ZDOPEN(STDIN_FILENO, mode);
- } else {
- qf->fp = QES_ZDOPEN(STDOUT_FILENO, mode);
- }
- } else {
- qf->fp = QES_ZOPEN(path, mode);
- }
- if (qf->fp == NULL) {
- (*onerr)("Opening file %s failed:\n%s\n", file, line,
- path, strerror(errno));
- qes_free(qf);
- return(NULL);
- }
- qf->mode = qes_file_guess_mode(mode);
- if (qf->mode == QES_FILE_MODE_UNKNOWN) {
- QES_ZCLOSE(qf->fp);
- qes_free(qf);
- return NULL;
- }
- qf->buffer = qes_calloc_(sizeof(*qf->buffer), QES_FILEBUFFER_LEN,
- onerr, file, line);
- if (qf->buffer == NULL) {
- QES_ZCLOSE(qf->fp);
- qes_free(qf);
- (*onerr)("Coudn't allocate buffer memory", file, line);
- return NULL;
- }
- qf->bufiter = qf->buffer;
- qf->buffer[0] = '\0';
- qf->bufend = qf->buffer;
- /* init struct fields */
- qf->eof = 0;
- qf->filepos = 0;
- qf->path = strndup(path, QES_MAX_FN_LEN);
- return(qf);
-}
-
-enum qes_file_mode
-qes_file_guess_mode (const char *mode)
-{
- if (mode[0] == 'r') {
- return QES_FILE_MODE_READ;
- } else if(mode[0] == 'w' || mode[0] == 'a') {
- return QES_FILE_MODE_WRITE;
- }
- return QES_FILE_MODE_UNKNOWN;
-}
-
-void
-qes_file_rewind (struct qes_file *file)
-{
- if (qes_file_ok(file)) {
- QES_ZSEEK(file->fp, 0, SEEK_SET);
- file->filepos = 0;
- file->eof = 0;
- file->feof = 0;
- file->bufiter = file->buffer;
- file->bufend = file->buffer;
- }
-}
-
-void
-qes_file_close_ (struct qes_file *file)
-{
- if (file != NULL) {
- if (file->fp != NULL) {
- QES_ZCLOSE(file->fp);
- }
- qes_free(file->path);
- qes_free(file->buffer);
- file->bufiter = NULL;
- file->bufend = NULL;
- qes_free(file);
- }
-}
-
-
-const char *
-qes_file_error (struct qes_file *file)
-{
- int error = 0;
- const char *errstr = "";
-
- if (!qes_file_ok(file)) {
- /* Never return NULL, or we'll SIGSEGV printf */
- return "BAD FILE";
- }
-#ifdef ZLIB_FOUND
- errstr = gzerror(file->fp, &error);
- if (error == Z_ERRNO) {
- return strerror(errno);
- }
-#else
- error = ferror(file->fp);
- if (error != 0) {
- errstr = strerror(errno);
- clearerr(file->fp);
- }
-#endif
- return errstr;
-}
-
-
-int
-qes_file_readable(struct qes_file *file)
-{
- /* Here we check that reads won't fail. We refil if we need to. */
- /* Can we possibly read from this file? */
- if (!qes_file_ok(file) || file->mode == QES_FILE_MODE_UNKNOWN || \
- file->mode == QES_FILE_MODE_WRITE || file->eof) {
- return 0;
- }
- /* We can read from buffer */
- if (file->bufiter < file->bufend && file->bufiter[0] != '\0') {
- return 1;
- }
- /* Buffer needs a refil */
- if (__qes_file_fill_buffer(file) != 0) {
- /* we either successfully refilled, or are at EOF */
- return file->eof ? EOF : 1;
- } else {
- /* No, we can't read */
- return 0;
- }
-}
-
-int
-qes_file_writable(struct qes_file *file)
-{
- /* Here we check that reads won't fail. We refil if we need to. */
- /* Can we possibly read from this file? */
- if (!qes_file_ok(file) || file->mode == QES_FILE_MODE_UNKNOWN || \
- file->mode == QES_FILE_MODE_READ) {
- return 0;
- }
- /* TODO: be more rigorous here */
- return 1;
-}
-
-int
-qes_file_peek(struct qes_file *file)
-{
- if (!qes_file_ok(file) || qes_file_readable(file) == 0) {
- return -2;
- } else if (file->eof) {
- return EOF;
- }
- return file->bufiter[0];
-}
-
-int
-qes_file_putstr(struct qes_file *stream, const struct qes_str *str)
-{
- /* TODO: use the buffer in write mode */
- return QES_ZWRITE(stream->fp, str->str, str->len);
-}
-
-int
-qes_file_puts(struct qes_file *file, const char *str)
-{
- if (!qes_file_ok(file) || !qes_file_writable(file)) {
- return -2;
- }
- return QES_ZFPUTS(file->fp, str);
-}
-
-int
-qes_file_putc(struct qes_file *file, const int chr)
-{
- int res = 0;
- if (!qes_file_ok(file) || !qes_file_writable(file)) {
- return -2;
- }
- res = QES_ZFPUTC(file->fp, chr);
- if (res != chr) {
- return -1;
- }
- return 1;
-}
-
-
-int
-qes_file_getc(struct qes_file *file)
-{
- if (!qes_file_ok(file) || qes_file_readable(file) == 0) {
- return -2;
- }
- if (file->eof) {
- return EOF;
- }
- return (file->bufiter++)[0];
-}
-
-ssize_t
-qes_file_getuntil_realloc_(struct qes_file *file, int delim, char **bufref,
- size_t *sizeref, qes_errhandler_func onerr,
- const char *src, const int line)
-{
- size_t len = 0;
- size_t tocpy = 0;
- char *buf = NULL;
- char *nextbuf = NULL;
- char *end = NULL;
- size_t size = 0;
- int ret = 0;
-
- if (bufref == NULL || !qes_file_ok(file) || sizeref == NULL) {
- return -2;
- }
- if (file->eof) {
- return EOF;
- }
- /* store local copies to stop dereferencing every time we need them */
- buf = *bufref;
- size = *sizeref;
- /* Alloc the buffer if it's NULL */
- if (buf == NULL) {
- buf = qes_malloc_(__INIT_LINE_LEN * sizeof(*buf), onerr, src, line);
- size = __INIT_LINE_LEN;
- buf[0] = '\0';
- }
- /* Set nextbuf AFTER we may/may not have alloced buf above
- * In case we error out below, we always set bufref = buf here, as
- * then we don't lose the memory alloced above */
- *bufref = nextbuf = buf;
- /* Read until delim is in file->buffer, filling buffer */
- while ((end = memchr(file->bufiter, delim, file->bufend - file->bufiter))
- == NULL) {
- /* copy the remainder of the buffer */
- tocpy = file->bufend - file->bufiter;
- len += tocpy;
- while (len + 1 >= size) {
- size = qes_roundupz(size);
- buf = qes_realloc_(buf, sizeof(*buf) * size, onerr, src, line);
- if (buf == NULL) {
- /* We bail out here, and *bufref is untouched. This means we
- * can check for errors, and free *bufref from the calling
- * function */
- return -2;
- }
- *bufref = buf;
- }
- /* set to the correct position in the NEW buf, maybe after realloc */
- nextbuf = buf + len - tocpy;
- memcpy(nextbuf, file->bufiter, tocpy);
- /* Update pointers to point to their respective heads */
- nextbuf += tocpy;
- file->bufiter += tocpy;
- /* Null-terminate buf */
- buf[len] = '\0';
- /* file->buffer should now be empty, so fill 'er up! */
- ret = __qes_file_fill_buffer(file);
- if (ret == 0) {
- /* Couln't fill, error out */
- return -2;
- } else if (ret == EOF) {
- /* EOF time */
- break;
- }
- }
- if (end != NULL) {
- /* We've got the delimter in the buffer */
- tocpy = end + 1 - file->bufiter; /* +1 includes the delimiter */
- } else if (file->bufiter < file->bufend) {
- /* No delimiter, but we return what we have. */
- tocpy = file->bufend - file->bufiter;
- } else {
- /* Nothign left at all */
- file->eof = 1;
- goto done;
- }
- /* we need to ensure that we still have enough room.
- * This happens as above */
- len += tocpy;
- while (len + 1 >= size) {
- size = qes_roundupz(size + 1);
- buf = qes_realloc_(buf, sizeof(*buf) * size, onerr, src, line);
- if (buf == NULL) {
- /* We bail out here, and *bufref is untouched. This means we
- * can check for errors, and free *bufref from the calling
- * function */
- return -2;
- }
- *bufref = buf;
- }
- nextbuf = buf + len - tocpy;
- memcpy(nextbuf, file->bufiter, tocpy);
- file->bufiter += tocpy;
- /* We don't bother updating nextbuf, as this was our final copy to buf */
- goto done;
-done:
- /* restore/update referred values */
- *bufref = buf;
- *sizeref = size;
- if (len > 0) {
- /* We have something to return, so return its length */
- file->filepos += len;
- buf[len] = '\0';
- return len;
- } else if (file->eof) {
- return EOF;
- } else {
- /* Shouldn't reach here! */
- return -2;
- }
-}
-#define qes_file_getuntil_realloc(fp, dlm, buf, sz) \
- qes_file_getuntil_realloc_(fp, dlm, buf, sz, QES_DEFAULT_ERR_FN, \
- __FILE__, __LINE__)
-#define qes_file_getuntil_realloc_errnil(fp, dlm, buf, sz) \
- qes_file_getuntil_realloc_(fp, dlm, buf, sz, errnil, __FILE__, __LINE__)
-#define qes_file_getuntil_realloc_errprint(fp, dlm, buf, sz) \
- qes_file_getuntil_realloc_(fp, dlm, buf, sz, errprint, __FILE__, __LINE__)
-#define qes_file_getuntil_realloc_errprintexit(fp, dlm, buf, sz) \
- qes_file_getuntil_realloc_(fp, dlm, buf, sz, errprintexit, __FILE__, \
- __LINE__)
-
-
-/* === FUNCTION =============================================================
- Name: qes_file_readline_realloc
- Description: Read a line from `file` into a `char *` pointed to by `buf`.
- This function has the added benefit of `realloc`-ing `buf`
- to the next highest base-2 power, if we run out of space.
- If it is realloced, `(*size)` is updated to the new buffer
- size. DON'T USE ON STACK BUFFERS.
- Returns: ssize_t set to either the length of the line copied to `*buf`,
- or one of -1 (EOF) or -2 (error).
- * ==========================================================================*/
-ssize_t
-qes_file_readline_realloc_ (struct qes_file *file, char **buf, size_t *size,
- qes_errhandler_func onerr, const char *src, const int line)
-{
- return qes_file_getuntil_realloc_(file, '\n', buf, size, onerr, src, line);
-}
-#define qes_file_readline_realloc(fp, buf, sz) \
- qes_file_readline_realloc_(fp, buf, sz, QES_DEFAULT_ERR_FN, __FILE__, \
- __LINE__)
-#define qes_file_readline_realloc_errnil(fp, buf, sz) \
- qes_file_readline_realloc_(fp, buf, sz, errnil, __FILE__, __LINE__)
-#define qes_file_readline_realloc_errprint(fp, buf, sz) \
- qes_file_readline_realloc_(fp, buf, sz, errprint, __FILE__, __LINE__)
-#define qes_file_readline_realloc_errprintexit(fp, buf, sz) \
- qes_file_readline_realloc_(fp, buf, sz, errprintexit, __FILE__, __LINE__)
-
-
-/*=== FUNCTION ============================================================*
-Name: qes_file_getuntil
-Parameters: struct qes_file *file: File to read
- const int delim: Delimiter char.
-Description: Reads ``file`` into ``dest`` until ``delim`` is found or
- ``maxlen - `` bytes have been read. ``delim`` is copied into
- ``dest``! ``delim`` can be EOF for "read until EOF", or any
- other thing that fits in a ``char``.
-Returns: ssize_t: EOF, -2 (error) or size of data read.
- *===========================================================================*/
-ssize_t
-qes_file_getuntil (struct qes_file *file, const int delim, char *dest,
- size_t maxlen)
-{
- size_t len = 0;
- char *nextbuf = dest;
- size_t tocpy = 0;
- char *end = NULL;
- int ret = 0 ;
- if (dest == NULL || !qes_file_ok(file) || maxlen < 1 || delim > 255) {
- /* EOF is normally == -1, so use -2 to differentiate them */
- return -2;
- }
- /* For detailed commentary, see qes_file_getuntil_realloc */
- /* Get out early if we're at EOF already */
- if (file->eof) {
- return EOF;
- }
- while ((end = memchr(file->bufiter, delim, file->bufend - file->bufiter))
- == NULL) {
- tocpy = file->bufend - file->bufiter;
- if (len + tocpy >= maxlen) {
- /* + 1 because we always leave space for \0 */
- tocpy += maxlen - (len + tocpy + 1);
- }
- len += tocpy;
- memcpy(nextbuf, file->bufiter, tocpy);
- nextbuf += tocpy;
- file->bufiter += tocpy;
- dest[len] = '\0'; /* Null-terminate buf */
- ret = __qes_file_fill_buffer(file);
- if (ret == 0) {
- return -2;
- } else if (ret == EOF) {
- break;
- }
- }
- if (end != NULL) {
- tocpy = (end - file->bufiter) + 1; /* +1 includes the delimiter */
- } else if (file->bufiter < file->bufend) {
- tocpy = file->bufend - file->bufiter;
- } else {
- /* Nothign left at all */
- file->eof = 1;
- goto done;
- }
- if (len + tocpy >= maxlen) {
- /* maxlen - 1 because we always leave space for \0 */
- tocpy += maxlen - (len + tocpy + 1);
- }
- memcpy(nextbuf, file->bufiter, tocpy);
- len += tocpy;
- file->bufiter += tocpy;
- goto done;
-done:
- if (len > 0) {
- file->filepos += len;
- dest[len] = '\0';
- return len;
- } else if (file->eof) {
- return EOF;
- } else {
- return -2;
- }
-}
-
-ssize_t
-qes_file_readline (struct qes_file *file, char *dest, size_t maxlen)
-{
- return qes_file_getuntil(file, '\n', dest, maxlen);
-}
-
-ssize_t
-qes_file_readline_str (struct qes_file *file, struct qes_str *str)
-{
- ssize_t len = 0;
-
- if (file == NULL || !qes_str_ok(str)) {
- return -2; /* ERROR, not EOF */
- }
- len = qes_file_readline_realloc(file, &(str->str), &(str->capacity));
- if (len < 0) {
- qes_str_nullify(str);
- return len;
- }
- str->len = len;
- return len;
-}
diff --git a/src/libqes/src/qes_file.h b/src/libqes/src/qes_file.h
deleted file mode 100644
index 341d39e..0000000
--- a/src/libqes/src/qes_file.h
+++ /dev/null
@@ -1,229 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: qes_file.h
- *
- * Description: Compressed file IO
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#ifndef QES_FILE_H
-#define QES_FILE_H
-
-#include <qes_util.h>
-#include <qes_str.h>
-
-enum qes_file_mode {
- QES_FILE_MODE_UNKNOWN,
- QES_FILE_MODE_READ,
- QES_FILE_MODE_WRITE
-};
-
-struct qes_file {
- QES_ZTYPE fp;
- char *path;
- char *buffer;
- char *bufiter;
- char *bufend;
- off_t filepos;
- enum qes_file_mode mode;
- /* Is the fp at EOF, AND do we have nothing left to copy from the buffer */
- int eof;
- /* Is the fp at EOF */
- int feof;
-};
-
-/* qes_file_open:
- Create a `struct qes_file` and open `path` with mode `mode` and
- errorhandler `onerr`
- */
-struct qes_file *qes_file_open_(const char *path,
- const char *mode,
- qes_errhandler_func onerr,
- const char *file,
- int line);
-#define qes_file_open(pth, mod) \
- qes_file_open_(pth, mod, QES_DEFAULT_ERR_FN, __FILE__, __LINE__)
-#define qes_file_open_errnil(pth, mod) \
- qes_file_open_(pth, mod, errnil, __FILE__, __LINE__)
-#define qes_file_open_errprint(pth, mod) \
- qes_file_open_(pth, mod, errprint, __FILE__, __LINE__)
-#define qes_file_open_errprintexit(pth, mod) \
- qes_file_open_(pth, mod, errprintexit, __FILE__, __LINE__)
-
-
-/*=== FUNCTION ============================================================*
-Name: qes_file_close
-Parameters: struct qes_file *file: file to close.
-Description: Closes the file pointer in ``file``, frees dynamically
- allocated members of ``file`` and sets ``file`` to NULL.
-Returns: void
- *===========================================================================*/
-void qes_file_close_ (struct qes_file *file);
-#define qes_file_close(file) do { \
- qes_file_close_ (file); \
- file = NULL; \
- } while(0)
-
-int qes_file_readable (struct qes_file *file);
-int qes_file_writable (struct qes_file *file);
-enum qes_file_mode qes_file_guess_mode
- (const char *mode);
-
-void qes_file_rewind (struct qes_file *file);
-int qes_file_peek (struct qes_file *file);
-
-int qes_file_putstr (struct qes_file *stream,
- const struct qes_str *str);
-int qes_file_puts (struct qes_file *file,
- const char *str);
-int qes_file_putc (struct qes_file *stream,
- const int chr);
-int qes_file_getc (struct qes_file *file);
-
-
-/*=== FUNCTION ============================================================*
-Name: qes_file_readline
-Parameters: struct qes_file *file: File to read
- char *dest: Destination buffer
- size_t maxlen: size of destination buffer
-Description: Reads at most ``maxlen - 1`` bytes of the next '\n' delimited
- line into ``dest``, and null- terminates ``dest``. The '\n' is
- copied, and therefore counts towards ``strlen()`` of ``dest``.
-Returns: ssize_t: EOF, -2 (error), or length of bytes copied, i.e.
- ``strlen(dest);``
- *===========================================================================*/
-ssize_t qes_file_readline (struct qes_file *file,
- char *dest,
- size_t maxlen);
-
-/*=== FUNCTION ============================================================*
-Name: qes_file_readline_str
-Parameters: struct qes_file *file: File to read.
- struct qes_str *str: struct qes_str object to read into.
-Description: Convenience wrapper around qes_file_readline_realloc, which
- reads a line into a struct qes_str object, passing str->str to
- and str->capacity to qes_file_readline_realloc.
-Returns: ssize_t set to either the length of the line copied to the
- struct qes_str, or one of -1 (EOF) or -2 (error).
-* ===========================================================================*/
-ssize_t qes_file_readline_str (struct qes_file *file,
- struct qes_str *str);
-
-/*=== FUNCTION ============================================================*
-Name: qes_file_getuntil
-Parameters: struct qes_file *file: File to read
- const int delim: Delimiter char.
-Description: Reads ``file`` into ``dest`` until ``delim`` is found or
- ``maxlen - `` bytes have been read. ``delim`` is copied into
- ``dest``! ``delim`` can be EOF for "read until EOF", or any
- other thing that fits in a ``char``.
-Returns: ssize_t: EOF, -2 (error) or size of data read.
- *===========================================================================*/
-ssize_t qes_file_getuntil (struct qes_file *file,
- const int delim,
- char *dest,
- size_t maxlen);
-
-/*=== FUNCTION ============================================================*
-Name: qes_file_getuntil_realloc
-Parameters: qes_file *file: File to read.
- int delim: Delimiter char.
- char **bufref: reference to a `char *` containing the buffer.
- Must not refer to a ``char[]`` that cannot be resized with
- ``realloc``.
- size *sizeref: Reference to a variable tracking the allocated
- size of the ``char *`` referred to by ``bufref``.
-Description: Read a string from `file` into a
- `char *` pointed to by
- `bufref` up to and inclding the character ``delim``. This
- function has the added benefit of `realloc`-ing `*bufref` to
- the next highest base-2 power, if we run out of space. If it
- is realloced, `(*sizeref)` is updated to the new buffer size.
-Returns: ssize_t set to either the length of the line copied to
- `*bufref`, or one of -1 (EOF) or -2 (error).
-*============================================================================*/
-ssize_t qes_file_getuntil_realloc_
- (struct qes_file *file,
- int delim,
- char **bufref,
- size_t *sizeref,
- qes_errhandler_func onerr,
- const char *src,
- const int line);
-
-#define qes_file_getuntil_realloc(fp, dlm, buf, sz) \
- qes_file_getuntil_realloc_(fp, dlm, buf, sz, QES_DEFAULT_ERR_FN, \
- __FILE__, __LINE__)
-#define qes_file_getuntil_realloc_errnil(fp, dlm, buf, sz) \
- qes_file_getuntil_realloc_(fp, dlm, buf, sz, errnil, __FILE__, __LINE__)
-#define qes_file_getuntil_realloc_errprint(fp, dlm, buf, sz) \
- qes_file_getuntil_realloc_(fp, dlm, buf, sz, errprint, __FILE__, __LINE__)
-#define qes_file_getuntil_realloc_errprintexit(fp, dlm, buf, sz) \
- qes_file_getuntil_realloc_(fp, dlm, buf, sz, errprintexit, __FILE__, \
- __LINE__)
-
-
-/* === FUNCTION =============================================================
- Name: qes_file_readline_realloc
- Description: Read a line from `file` into a `char *` pointed to by `buf`.
- This function has the added benefit of `realloc`-ing `buf`
- to the next highest base-2 power, if we run out of space.
- If it is realloced, `(*size)` is updated to the new buffer
- size. DON'T USE ON STACK BUFFERS.
- Returns: ssize_t set to either the length of the line copied to `*buf`,
- or one of -1 (EOF) or -2 (error).
- * ==========================================================================*/
-ssize_t qes_file_readline_realloc_
- (struct qes_file *file,
- char **buf,
- size_t *size,
- qes_errhandler_func onerr,
- const char *src,
- const int line);
-#define qes_file_readline_realloc(fp, buf, sz) \
- qes_file_readline_realloc_(fp, buf, sz, QES_DEFAULT_ERR_FN, __FILE__, \
- __LINE__)
-#define qes_file_readline_realloc_errnil(fp, buf, sz) \
- qes_file_readline_realloc_(fp, buf, sz, errnil, __FILE__, __LINE__)
-#define qes_file_readline_realloc_errprint(fp, buf, sz) \
- qes_file_readline_realloc_(fp, buf, sz, errprint, __FILE__, __LINE__)
-#define qes_file_readline_realloc_errprintexit(fp, buf, sz) \
- qes_file_readline_realloc_(fp, buf, sz, errprintexit, __FILE__, __LINE__)
-
-
-const char *qes_file_error (struct qes_file *file);
-
-static inline int
-qes_file_ok (const struct qes_file *qf)
-{
- /* qes_file_ok just check we won't dereference NULLs, so we check pointer
- * NULLness for all pointers we care about in current modes. Which, unless
- * we're Write-only, is all of them */
- return qf != NULL && \
- qf->fp != NULL && \
- qf->bufiter != NULL && \
- qf->buffer != NULL;
-}
-
-
-#endif /* QES_FILE_H */
diff --git a/src/libqes/src/qes_libgnu.c b/src/libqes/src/qes_libgnu.c
deleted file mode 100644
index 1d6d88a..0000000
--- a/src/libqes/src/qes_libgnu.c
+++ /dev/null
@@ -1,32 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: qes_libgnu.c
- * Description: Functions required from gnulib
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "qes_libgnu.h"
-
-#ifndef ZLIB_FOUND
-# include "crc.c"
-#endif
diff --git a/src/libqes/src/qes_libgnu.h b/src/libqes/src/qes_libgnu.h
deleted file mode 100644
index 17b7a78..0000000
--- a/src/libqes/src/qes_libgnu.h
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: qes_libgnu.h
- * Description: Functions required from gnulib
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#ifndef QES_LIBGNU_H
-#define QES_LIBGNU_H
-
-#include "qes_config.h"
-
-/* This file and qes_libgnu.c are designed to allow us to keep the sources of
- * the gnulib functions intact and in their original separate form. */
-
-#ifndef ZLIB_FOUND
-# include "crc.h"
-#else
-# include <zlib.h>
-/* Cast is to avoid a difference in signed-ness in the two implementations. */
-# define crc32_update(c, b, l) crc32(c, (const unsigned char *)b, l)
-#endif
-
-#endif /* QES_LIBGNU_H */
diff --git a/src/libqes/src/qes_log.c b/src/libqes/src/qes_log.c
deleted file mode 100644
index 49a2103..0000000
--- a/src/libqes/src/qes_log.c
+++ /dev/null
@@ -1,267 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: qes_log.c
- *
- * Description: Logging module of libngs2
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "qes_log.h"
-
-
-struct qes_logger *
-qes_logger_create(void)
-{
- return qes_calloc(1, sizeof(struct qes_logger));
-}
-
-int
-qes_logger_init(struct qes_logger *logger,
- const char *name,
- enum qes_log_level level)
-{
- if (logger == NULL) return 1;
-
- if (name != NULL) {
- logger->name = strdup(name);
- } else if (logger->name != NULL) {
- free(logger->name);
- logger->name = NULL;
- }
- logger->level = level;
- return 0;
-}
-
-int
-qes_logger_add_destination_formatted(struct qes_logger *logger,
- FILE *stream,
- enum qes_log_level level,
- char *(*formatter)(struct qes_log_entry *entry))
-{
- struct qes_log_destination *new = NULL;
- size_t new_sz = logger->n_destinations + 1;
-
- new = qes_realloc(logger->destinations,
- new_sz * sizeof(*logger->destinations));
- if (new == NULL) {
- return 1;
- }
- logger->destinations = new;
- logger->n_destinations = new_sz;
- /* For ease of reference, save the ptr to the (new) final struct in
- * the array */
- new = &new[new_sz - 1];
- new->stream = stream;
- new->level = level;
- new->formatter = formatter;
- return 0;
-}
-
-void
-_qes_logger_destroy(struct qes_logger *logger)
-{
- if (logger != NULL) {
- qes_free(logger->name);
- qes_free(logger->destinations);
- qes_free(logger);
- }
-}
-
-struct qes_log_entry *
-qes_log_entry_create(void)
-{
- return qes_calloc(1, sizeof(struct qes_log_entry));
-}
-
-int
-qes_log_entry_init(struct qes_log_entry *entry,
- enum qes_log_level level,
- const char *message)
-{
- if (entry == NULL || message == NULL) return -1;
-
- entry->level = level;
- entry->message = strdup(message);
- return 0;
-}
-
-int
-qes_log_entry_format_va(struct qes_log_entry *entry,
- enum qes_log_level level,
- const char *format,
- va_list args)
-{
- int res = 0;
- char *message = NULL;
-
- /* Format the error message w/ user input */
- res = vasprintf(&message, format, args);
- if (res < 1) {
- /* Alloc inside vasprintf failed */
- return 1;
- }
- /* Make the entry struct */
- res = qes_log_entry_init(entry, level, message);
- free(message);
- return res;
-}
-
-int
-qes_log_entry_format(struct qes_log_entry *entry,
- enum qes_log_level level,
- const char *format,
- ...)
-{
- va_list args;
- int res = 0;
-
- /* Format the error message w/ user input */
- va_start(args, format);
- res = qes_log_entry_format_va(entry, level, format, args);
- va_end(args);
- return res;
-}
-
-void
-_qes_log_entry_destroy(struct qes_log_entry *entry)
-{
- if (entry != NULL) {
- qes_free(entry->message);
- qes_free(entry);
- }
-}
-void qes_log_entry_clear(struct qes_log_entry *entry)
-{
- if (entry != NULL) {
- qes_free(entry->message);
- entry->level = QES_LOG_DEBUG;
- }
-}
-
-int
-qes_logger_write_entry(struct qes_logger *logger,
- struct qes_log_entry *entry)
-{
- size_t iii;
- int res;
-
- if (logger == NULL || entry == NULL) return 1;
-
- /* Message is to unimportant for this logger */
- if (logger->level > entry->level) return 0;
-
- for (iii = 0; iii < logger->n_destinations; iii++) {
- char *formatted = NULL;
- struct qes_log_destination *dest = &logger->destinations[iii];
-
- /* Message is to unimportant for this destination */
- if (dest->level > entry->level) continue;
-
- formatted = dest->formatter(entry);
- if (formatted == NULL) return 1;
- res = fprintf(dest->stream, "%s", formatted);
- fflush(dest->stream);
- qes_free(formatted);
- if (res < 0) return 1;
- }
- return 0;
-}
-
-int
-qes_log_message(struct qes_logger *logger,
- enum qes_log_level level,
- const char *message)
-{
- struct qes_log_entry entry;
- int res = 0;
-
- res = qes_log_entry_format(&entry, level, "%s", message);
- if (res != 0) return res;
- res = qes_logger_write_entry(logger, &entry);
- qes_log_entry_clear(&entry);
- return res;
-}
-
-int
-qes_log_format(struct qes_logger *logger,
- enum qes_log_level level,
- const char *format,
- ...)
-{
- struct qes_log_entry entry;
- va_list args;
- int res = 0;
-
- va_start(args, format);
- res = qes_log_entry_format_va(&entry, level, format, args);
- va_end(args);
- if (res != 0) return res;
- res = qes_logger_write_entry(logger, &entry);
- qes_log_entry_clear(&entry);
- return res;
-}
-
-char *
-qes_log_formatter_plain(struct qes_log_entry *entry)
-{
- /* In the plain-text case, we just pass the message as is. */
- if (entry == NULL) return NULL;
- if (entry->message == NULL) return NULL;
- return strdup(entry->message);
-}
-
-char *
-qes_log_formatter_pretty(struct qes_log_entry *entry)
-{
- char *buf = NULL;
- const char *colour = ANSIRST;
- const char *reset = ANSIRST;
- char marker = ' ';
- int res = 0;
-
- if (entry == NULL || entry->message == NULL) return NULL;
-
- if (entry->level <= QES_LOG_DEBUG) {
- marker = '.';
- colour = ANSIBEG ATDIM FGCYN BGBLK ANSIEND;
- reset = "";
- } else if (entry->level <= QES_LOG_INFO) {
- marker = '*';
- colour = ANSIBEG ATNRM FGGRN BGBLK ANSIEND;
- } else if (entry->level <= QES_LOG_WARNING) {
- marker = '!';
- colour = ANSIBEG ATULN FGYEL BGBLK ANSIEND;
- } else if (entry->level <= QES_LOG_ERROR) {
- marker = 'E';
- colour = ANSIBEG ATBLD FGMAG BGBLK ANSIEND;
- } else {
- marker = 'F';
- colour = ANSIBEG ATBLD ATBNK FGRED BGBLK ANSIEND;
- }
- res = asprintf(&buf, "%s[%c] %s%s", colour, marker, entry->message, reset);
- if (res > 0) {
- return buf;
- } else {
- return NULL;
- }
-}
diff --git a/src/libqes/src/qes_log.h b/src/libqes/src/qes_log.h
deleted file mode 100644
index fe81088..0000000
--- a/src/libqes/src/qes_log.h
+++ /dev/null
@@ -1,166 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: qes_log.h
- *
- * Description: Logging module of libngs2
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#ifndef QES_LOG_H
-#define QES_LOG_H
-
-#include <stdlib.h>
-#include <stdio.h>
-#include <qes_util.h>
-
-#define ANSIBEG "\033["
-#define ANSIEND "m"
-
-#define ANSIRST ANSIBEG "0" ANSIEND
-
-#define ATNRM "0;"
-#define ATBLD "1;"
-#define ATDIM "2;"
-#define ATULN "3;"
-#define ATBNK "5;"
-#define ATREV "7;"
-#define ATHID "8;"
-
-#define FGBLK "30;"
-#define FGRED "31;"
-#define FGGRN "32;"
-#define FGYEL "33;"
-#define FGBLU "34;"
-#define FGMAG "35;"
-#define FGCYN "36;"
-#define FGWHT "37;"
-
-#define BGBLK "40"
-#define BGRED "41"
-#define BGGRN "42"
-#define BGYEL "43"
-#define BGBLU "44"
-#define BGMAG "45"
-#define BGCYN "46"
-#define BGWHT "47"
-
-enum qes_log_level {
- /* The idea is that the user can add values between these, if they need
- * to. a la Python's logging module. */
- QES_LOG_DEBUG = 0,
- QES_LOG_INFO = 10,
- QES_LOG_WARNING = 20,
- QES_LOG_ERROR = 30,
- QES_LOG_FATAL = 40,
-};
-
-typedef enum qes_log_level QesLogLevel;
-
-struct qes_log_entry {
- char *message;
- enum qes_log_level level;
-};
-
-typedef struct qes_log_entry QesLogEntry;
-struct qes_log_destination {
- FILE *stream;
- enum qes_log_level level;
- char *(*formatter)(struct qes_log_entry *entry);
-};
-typedef struct qes_log_destination QesLogDestination;
-
-struct qes_logger {
- struct qes_log_destination *destinations;
- size_t n_destinations;
- enum qes_log_level level;
- char *name;
- int lock;
-};
-typedef struct qes_logger QesLogger;
-
-
-struct qes_logger *qes_logger_create(void);
-int qes_logger_init(struct qes_logger *logger, const char *name,
- enum qes_log_level level);
-int qes_logger_add_destination_formatted(struct qes_logger *logger,
- FILE *stream,
- enum qes_log_level level,
- char *(*formatter)(struct qes_log_entry *entry));
-#define qes_logger_add_destination(log, stream, level) \
- qes_logger_add_destination_formatted(log, stream, level, \
- &qes_log_formatter_plain)
-void _qes_logger_destroy(struct qes_logger *logger);
-#define qes_logger_destroy(l) STMT_BEGIN _qes_logger_destroy(l); l = NULL; STMT_END
-
-
-struct qes_log_entry *qes_log_entry_create(void);
-int qes_log_entry_init(struct qes_log_entry *entry, enum qes_log_level level,
- const char *message);
-void qes_log_entry_clear(struct qes_log_entry *entry);
-
-char *qes_log_formatter_plain(struct qes_log_entry *entry);
-char *qes_log_formatter_pretty(struct qes_log_entry *entry);
-
-int qes_log_entry_format(struct qes_log_entry *entry, enum qes_log_level level,
- const char *format, ...);
-int qes_log_entry_format_va(struct qes_log_entry *entry,
- enum qes_log_level level, const char *format,
- va_list args);
-int qes_logger_write_entry(struct qes_logger *logger,
- struct qes_log_entry *entry);
-void _qes_log_entry_destroy(struct qes_log_entry *log_entry);
-#define qes_log_entry_destroy(l) STMT_BEGIN _qes_log_entry_destroy(l); l = NULL; STMT_END
-
-
-int qes_log_message(struct qes_logger *logger, enum qes_log_level level,
- const char *message);
-#ifndef NDEBUG
-#define qes_log_message_debug(log, msg) qes_log_message(log, QES_LOG_DEBUG, msg)
-#else
-#define qes_log_message_debug(log, msg)
-#endif
-#define qes_log_message_info(log, msg) qes_log_message(log, QES_LOG_INFO, msg)
-#define qes_log_message_warning(log, msg) qes_log_message(log, QES_LOG_WARNING, msg)
-#define qes_log_message_error(log, msg) qes_log_message(log, QES_LOG_ERROR, msg)
-#define qes_log_message_fatal(log, msg) qes_log_message(log, QES_LOG_FATAL, msg)
-
-
-int qes_log_format(struct qes_logger *logger, enum qes_log_level level,
- const char *format, ...);
-#ifndef NDEBUG
-#define qes_log_format_debug(log, fmt, ...) \
- qes_log_format(log, QES_LOG_DEBUG, fmt, __VA_ARGS__)
-#else
-#define qes_log_format_debug(log, fmt, ...)
-#endif
-#define qes_log_format_info(log, fmt, ...) \
- qes_log_format(log, QES_LOG_INFO, fmt, __VA_ARGS__)
-#define qes_log_format_warning(log, fmt, ...) \
- qes_log_format(log, QES_LOG_WARNING, fmt, __VA_ARGS__)
-#define qes_log_format_error(log, fmt, ...) \
- qes_log_format(log, QES_LOG_ERROR, fmt, __VA_ARGS__)
-#define qes_log_format_fatal(log, fmt, ...) \
- qes_log_format(log, QES_LOG_FATAL, fmt, __VA_ARGS__)
-
-
-#endif /* QES_LOG_H */
diff --git a/src/libqes/src/qes_match.c b/src/libqes/src/qes_match.c
deleted file mode 100644
index 6874734..0000000
--- a/src/libqes/src/qes_match.c
+++ /dev/null
@@ -1,99 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: qes_match.c
- *
- * Description: Sequence matching and finding functions used in
- * bioinformatic tasks
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "qes_match.h"
-
-
-inline int_fast32_t
-qes_match_hamming (const char *seq1, const char *seq2, size_t len)
-{
- int_fast32_t mismatches = 0;
- size_t iii = 0;
-
- /* Error out on bad arguments */
- if (seq1 == NULL || seq2 == NULL) {
- return -1;
- }
- /* If we've been given a length of 0, we make it up ourselves */
- if (len == 0) {
- size_t len2 = strlen(seq2);
- len = strlen(seq1);
- /* Max of len & len2 */
- if (len > len2) {
- len = len2;
- }
- }
- /* Count mismatches. See comment on analogous loop in qes_match_hamming_max
- * for an explanation. */
- while(iii < len) {
- if (seq2[iii] != seq1[iii]) {
- mismatches++;
- }
- iii++;
- }
- return mismatches;
-}
-
-
-inline int_fast32_t
-qes_match_hamming_max(const char *seq1, const char *seq2, size_t len,
- int_fast32_t max)
-{
- int_fast32_t mismatches = 0;
- size_t iii = 0;
-
- /* Error out on bad arguments */
- if (seq1 == NULL || seq2 == NULL || max < 0) {
- return -1;
- }
- /* If we've been given a length of 0, we make it up ourselves */
- if (len == 0) {
- size_t len2 = strlen(seq2);
- len = strlen(seq1);
- /* Max of len & len2 */
- if (len > len2) {
- len = len2;
- }
- }
- /* We obediently go until ``len``, assuming whoever gave us ``len`` knew
- WTF they were doing. This makes things a bit faster, since these
- functions are expected to be very much inner-loop. */
- while(iii < len) {
- /* Find mismatch count */
- if (seq2[iii] != seq1[iii]) {
- mismatches++;
- }
- iii++;
- if (mismatches > max) {
- /* Bail out if we're over max, always cap at max + 1 */
- return max + 1;
- }
- }
- return mismatches;
-}
diff --git a/src/libqes/src/qes_match.h b/src/libqes/src/qes_match.h
deleted file mode 100644
index 3098ea4..0000000
--- a/src/libqes/src/qes_match.h
+++ /dev/null
@@ -1,66 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: qes_match.h
- *
- * Description: Sequence matching and finding functions used in
- * bioinformatic tasks
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#ifndef QES_MATCH_H
-#define QES_MATCH_H
-
-#include <qes_util.h>
-
-
-/*=== FUNCTION ============================================================*
-Name: qes_match_hamming
-Parameters: const char *seq1, *seq2: Two strings to compare.
- size_t len: Compare ``len`` chars. If 0, guess length with
- strlen (may be unsafe).
-Description: Find the hamming distance between two strings. The strings are
- matched until the length of the smallest string.
-Returns: The hamming distance between ``seq1`` and ``seq2``, or -1 on
- error.
- *===========================================================================*/
-extern int_fast32_t qes_match_hamming(const char *seq1, const char *seq2, size_t len);
-
-
-/*=== FUNCTION ============================================================*
-Name: qes_match_hamming_max
-Parameters: const char *seq1, *seq2: Two strings to compare.
- size_t len: Compare ``len`` chars. If 0, guess length with
- strlen (may be unsafe).
- int_fast32_t max: Stop counting at ``max``, return ``max + 1``.
-Description: Find the hamming distance between two strings. The strings are
- matched until the length of the smallest string, or ``len``
- charachers, or until the maximum hamming distance (``max``) is
- reached.
-Returns: The hamming distance between ``seq1`` and ``seq2``, or
- ``max + 1`` if the hamming distance exceeds ``max``, or -1 on
- error.
- *===========================================================================*/
-extern int_fast32_t qes_match_hamming_max(const char *seq1, const char *seq2, size_t len,
- int_fast32_t max);
-
-#endif /* QES_MATCH_H */
diff --git a/src/libqes/src/qes_seq.c b/src/libqes/src/qes_seq.c
deleted file mode 100644
index f9e8e61..0000000
--- a/src/libqes/src/qes_seq.c
+++ /dev/null
@@ -1,232 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: qes_seq.c
- *
- * Description: Sequence structures
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "qes_seq.h"
-
-
-void
-qes_seq_init (struct qes_seq *seq)
-{
- qes_str_init(&seq->name, __INIT_LINE_LEN);
- qes_str_init(&seq->comment, __INIT_LINE_LEN);
- qes_str_init(&seq->seq, __INIT_LINE_LEN);
- qes_str_init(&seq->qual, __INIT_LINE_LEN);
-}
-
-struct qes_seq *
-qes_seq_create (void)
-{
- struct qes_seq *seq = qes_malloc(sizeof(*seq));
-
- qes_str_init(&seq->name, __INIT_LINE_LEN);
- qes_str_init(&seq->comment, __INIT_LINE_LEN);
- qes_str_init(&seq->seq, __INIT_LINE_LEN);
- qes_str_init(&seq->qual, __INIT_LINE_LEN);
- return seq;
-}
-
-struct qes_seq *
-qes_seq_create_no_qual (void)
-{
- struct qes_seq *seq = qes_malloc(sizeof(*seq));
-
- qes_str_init(&seq->name, __INIT_LINE_LEN);
- qes_str_init(&seq->comment, __INIT_LINE_LEN);
- qes_str_init(&seq->seq, __INIT_LINE_LEN);
- seq->qual.capacity = 0;
- seq->qual.len = 0;
- seq->qual.str = NULL;
- return seq;
-}
-
-struct qes_seq *
-qes_seq_create_no_qual_or_comment (void)
-{
- struct qes_seq *seq = qes_malloc(sizeof(*seq));
- qes_str_init(&seq->name, __INIT_LINE_LEN);
- qes_str_init(&seq->seq, __INIT_LINE_LEN);
- seq->qual.capacity = 0;
- seq->qual.len = 0;
- seq->qual.str = NULL;
- seq->comment.capacity = 0;
- seq->comment.len = 0;
- seq->comment.str = NULL;
- return seq;
-}
-
-
-inline int
-qes_seq_fill_name (struct qes_seq *seqobj, const char *name, size_t len)
-{
- if (seqobj == NULL || name == NULL || len < 1) {
- return 1;
- }
- qes_str_fill_charptr(&seqobj->name, name, len);
- return 0;
-}
-
-inline int
-qes_seq_fill_comment (struct qes_seq *seqobj, const char *comment, size_t len)
-{
- if (seqobj == NULL || comment == NULL || len < 1) {
- return 1;
- }
- qes_str_fill_charptr(&seqobj->comment, comment, len);
- return 0;
-}
-
-inline int
-qes_seq_fill_seq (struct qes_seq *seqobj, const char *seq, size_t len)
-{
- if (seqobj == NULL || seq == NULL || len < 1) {
- return 1;
- }
- qes_str_fill_charptr(&seqobj->seq, seq, len);
- return 0;
-}
-
-inline int
-qes_seq_fill_qual (struct qes_seq *seqobj, const char *qual, size_t len)
-{
- if (seqobj == NULL || qual == NULL || len < 1) {
- return 1;
- }
- qes_str_fill_charptr(&seqobj->qual, qual, len);
- return 0;
-}
-
-inline int
-qes_seq_fill_header (struct qes_seq *seqobj, char *header, size_t len)
-{
- char *tmp = NULL;
- size_t startfrom = 0;
-
- if (seqobj == NULL || header == NULL) {
- return 1;
- }
- if (len < 1) {
- len = strlen(header);
- }
- while (isspace(header[len-1])) {
- header[--len] = '\0';
- }
- tmp = memchr(header, ' ', len);
- startfrom = header[0] == '@' || header[0] == '>' ? 1 : 0;
- if (tmp != NULL) {
- qes_str_fill_charptr(&seqobj->name, header + startfrom,
- tmp - header - startfrom);
- qes_str_fill_charptr(&seqobj->comment, tmp + 1, 0);
- } else {
- qes_str_fill_charptr(&seqobj->name, header + startfrom, len - startfrom);
- qes_str_nullify(&seqobj->comment);
- }
- return 0;
-}
-
-inline int
-qes_seq_fill(struct qes_seq *seqobj, const char *name, const char *comment,
- const char *seq, const char *qual)
-{
- if (!qes_seq_ok(seqobj) || name == NULL || comment == NULL || seq == NULL \
- || qual == NULL) {
- return 1;
- }
- qes_str_nullify(&seqobj->name);
- qes_str_nullify(&seqobj->comment);
- qes_str_nullify(&seqobj->seq);
- qes_str_nullify(&seqobj->qual);
- if (qes_seq_fill_name(seqobj, name, strlen(name)) != 0) return 1;
- if (qes_seq_fill_comment(seqobj, comment, strlen(comment)) != 0) return 1;
- if (qes_seq_fill_seq(seqobj, seq, strlen(seq)) != 0) return 1;
- if (strlen(qual) > 0 &&
- qes_seq_fill_qual(seqobj, qual, strlen(qual)) != 0) return 1;
- return 0;
-}
-
-/*=== FUNCTION ============================================================*
-Name: qes_seq_destroy
-Parameters: struct qes_seq *: seq to destroy.
-Description: Deallocate and set to NULL a struct qes_seq on the heap.
-Returns: void.
- *===========================================================================*/
-void
-qes_seq_destroy_(struct qes_seq *seq)
-{
- if (seq != NULL) {
- qes_str_destroy_cp(&seq->name);
- qes_str_destroy_cp(&seq->comment);
- qes_str_destroy_cp(&seq->seq);
- qes_str_destroy_cp(&seq->qual);
- qes_free(seq);
- }
-}
-
-static inline void
-_printstr_linewrap(const struct qes_str *str, size_t linelen, FILE *stream)
-{
-
- for (size_t i = 0; i < str->len; i += linelen) {
- const size_t remaining = str->len - i;
- const size_t towrite = remaining < linelen ? remaining : linelen;
- fwrite(str->str + i, towrite, 1, stream);
- fputc('\n', stream);
- }
-}
-
-int
-qes_seq_print(const struct qes_seq *seq, FILE *stream, bool fasta, int tag)
-{
- if (!qes_seq_ok(seq)) return 1;
- if (stream == NULL) return 1;
- size_t linelen = fasta ? 79 : SIZE_MAX - 1;
-
- if (fasta) {
- fputc('>', stream);
- } else {
- fputc('@', stream);
- }
- fputs(seq->name.str, stream);
- if (tag > 0) {
- // Add tag only if read is not already tagged.
- if (seq->name.len > 2 && seq->name.str[seq->name.len - 2] != '/') {
- fprintf(stream, "/%d", tag);
- }
- }
- if (seq->comment.str) {
- fputc(' ', stream);
- fputs(seq->comment.str, stream);
- }
- fputc('\n', stream);
- _printstr_linewrap(&seq->seq, linelen, stream);
- if (!fasta) {
- fputs("+\n", stream);
- _printstr_linewrap(&seq->qual, linelen, stream);
- }
- fflush(stream);
- return 0;
-}
diff --git a/src/libqes/src/qes_seq.h b/src/libqes/src/qes_seq.h
deleted file mode 100644
index f2a1b46..0000000
--- a/src/libqes/src/qes_seq.h
+++ /dev/null
@@ -1,219 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: qes_seq.h
- *
- * Description: Sequence structures
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#ifndef QES_SEQ_H
-#define QES_SEQ_H
-
-#include <stdbool.h>
-#include <qes_util.h>
-#include <qes_str.h>
-
-
-/*---------------------------------------------------------------------------
- | qes_seq module -- data structures to hold NGS sequences |
- ---------------------------------------------------------------------------*/
-
-/* TYPE DEFINITIONS */
-struct qes_seq {
- struct qes_str name;
- struct qes_str comment;
- struct qes_str seq;
- struct qes_str qual;
-};
-
-/* PROTOTYPES */
-
-/*=== FUNCTION ============================================================*
-Name: qes_seq_create
-Parameters: void
-Description: Create a ``struct qes_seq`` object on the heap, creating and
- initialising all members. qes_seq_create_no_X functions do not
- create or initialise the members in their names.
-Returns: struct qes_seq *: A non-null memory address on success, otherwise NULL.
- *===========================================================================*/
-struct qes_seq *qes_seq_create (void);
-struct qes_seq *qes_seq_create_no_qual (void);
-struct qes_seq *qes_seq_create_no_qual_or_comment (void);
-
-void qes_seq_init (struct qes_seq *seq);
-
-/*=== FUNCTION ============================================================*
-Name: qes_seq_ok
-Parameters: struct qes_seq *: seq to check
-Description: Check if ``seq`` is a usable struct qes_seq struct. qes_seq_ok_no-X
- functions permit the member(s) in their names to be unusable.
-Returns: 1 if usable, 0 otherwise.
- *===========================================================================*/
-static inline int
-qes_seq_ok (const struct qes_seq *seq)
-{
- return \
- seq != NULL && \
- qes_str_ok(&seq->name) && \
- qes_str_ok(&seq->comment) && \
- qes_str_ok(&seq->seq) && \
- qes_str_ok(&seq->qual);
-}
-
-static inline int
-qes_seq_ok_no_comment (const struct qes_seq *seq)
-{
- return \
- seq != NULL && \
- qes_str_ok(&seq->name) && \
- qes_str_ok(&seq->seq) && \
- qes_str_ok(&seq->qual);
-}
-
-static inline int
-qes_seq_ok_no_qual (const struct qes_seq *seq)
-{
- return \
- seq != NULL && \
- qes_str_ok(&seq->name) && \
- qes_str_ok(&seq->comment) && \
- qes_str_ok(&seq->seq);
-}
-
-static inline int
-qes_seq_ok_no_comment_or_qual (const struct qes_seq *seq)
-{
- return \
- seq != NULL && \
- qes_str_ok(&seq->name) && \
- qes_str_ok(&seq->seq);
-}
-
-static inline int
-qes_seq_has_comment (const struct qes_seq *seq)
-{
- return qes_seq_ok(seq) && seq->comment.len > 0;
-}
-
-static inline int
-qes_seq_has_qual (const struct qes_seq *seq)
-{
- return qes_seq_ok(seq) && seq->qual.len > 0;
-}
-
-static inline int
-qes_seq_n_bytes (const struct qes_seq *seq)
-{
- if (!qes_seq_ok(seq)) {
- return -1;
- }
- /* Arragned per line in a fastq */
- return 1 + seq->name.len + \
- (qes_seq_has_comment(seq) ? 1 + seq->comment.len : 0) + 1 + \
- seq->seq.len + 1 +\
- qes_seq_has_qual(seq) ? 2 + seq->qual.len + 1 : 0;
-}
-
-static inline int
-qes_seq_truncate (struct qes_seq *seq, const size_t at)
-{
- if (!qes_seq_ok(seq)) return -1;
-
- int res = 0;
- res = qes_str_truncate(&seq->seq, at);
- if (res != 0) return res;
-
- res = qes_str_truncate(&seq->qual, at);
- return res;
-}
-
-/*=== FUNCTION ============================================================*
-Name: qes_seq_fill_header
-Parameters: struct qes_seq *seqobj: Seq object that will receive the header.
-Description: Fills the name and comment members of a ``struct qes_seq`` from the
- header line of a fasta/fastq file.
-Returns: int: 1 on success, otherwise 0 for failure.
- *===========================================================================*/
-extern int qes_seq_fill_header(struct qes_seq *seqobj, char *header, size_t len);
-
-
-/*=== FUNCTION ============================================================*
-Name: qes_seq_fill_X
-Parameters: These functions take a ``struct qes_seq``, a char array and
- the length of the char array as a size_t.
-Description: Fill a struct qes_seq's name, comment, seq or qual member from
- a char array. If a non-zero value is given to ``len``, it is
- assumed to be the length of the string, otherwise the length of
- the string is calculated using strlen.
-Returns: int: 1 on success, 0 on failure.
- *===========================================================================*/
-extern int qes_seq_fill_name(struct qes_seq *seqobj, const char *name,
- size_t len);
-extern int qes_seq_fill_comment(struct qes_seq *seqobj, const char *comment,
- size_t len);
-extern int qes_seq_fill_seq(struct qes_seq *seqobj, const char *seq,
- size_t len);
-extern int qes_seq_fill_qual(struct qes_seq *seqobj, const char *qual,
- size_t len);
-extern int qes_seq_fill(struct qes_seq *seqobj, const char *name,
- const char *comment, const char *seq, const char *qual);
-
-/*=== FUNCTION ============================================================*
-Name: qes_seq_print
-Parameters: const struct qes_seq *seq: seq to print
- FILE *stream: open file stream to print to.
- bool fasta: Print as fasta?
- int tag: Tag read name with /%d. use 0 to disable.
-Description: Print ``seq`` in formatted per ``format`` to ``stream``.
-Returns: int: 1 on success, 0 on failure.
- *===========================================================================*/
-int qes_seq_print (const struct qes_seq *seq,
- FILE *stream,
- bool fasta,
- int tag);
-
-/*=== FUNCTION ============================================================*
-Name: qes_seq_destroy
-Parameters: struct qes_seq *: seq to destroy.
-Description: Deallocate and set to NULL a struct qes_seq on the heap.
-Returns: void.
- *===========================================================================*/
-void qes_seq_destroy_(struct qes_seq *seq);
-#define qes_seq_destroy(seq) do { \
- qes_seq_destroy_(seq); \
- seq = NULL; \
- } while(0)
-
-static inline int
-qes_seq_copy(struct qes_seq *dest, const struct qes_seq *src)
-{
- if (dest == src || !qes_seq_ok(dest) || !qes_seq_ok(src)) return 1;
-
- if (qes_str_copy(&dest->name, &src->name) != 0) return 1;
- if (qes_str_copy(&dest->comment, &src->comment) != 0) return 1;
- if (qes_str_copy(&dest->seq, &src->seq) != 0) return 1;
- if (qes_str_copy(&dest->qual, &src->qual) != 0) return 1;
- return 0;
-}
-
-#endif /* QES_SEQ_H */
diff --git a/src/libqes/src/qes_seqfile.c b/src/libqes/src/qes_seqfile.c
deleted file mode 100644
index 469ec3b..0000000
--- a/src/libqes/src/qes_seqfile.c
+++ /dev/null
@@ -1,327 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: qes_seqfile.c
- *
- * Description: qes_seqfile -- read sequences in FASTA or FASTQ format.
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "qes_seqfile.h"
-
-
-static inline ssize_t
-read_fastq_seqfile(struct qes_seqfile *seqfile, struct qes_seq *seq)
-{
- /* Convenience macro, this happens a lot */
-#define CHECK_AND_TRIM(subrec) if (len < 1) { \
- goto error; \
- } else { \
- subrec.str[--len] = '\0'; \
- subrec.len = len; \
- }
- ssize_t len = 0;
- int next = '\0';
- int errcode = -1;
-
- /* Fast-forward past the delimiter '@', ensuring it exists */
- next = qes_file_getc(seqfile->qf);
- if (next == EOF) {
- return EOF;
- } else if (next != FASTQ_DELIM) {
- /* This ain't a fastq! WTF! */
- errcode = -3;
- goto error;
- }
- len = qes_file_readline_str(seqfile->qf, &seqfile->scratch);
- if (len < 1) {
- /* Weird truncated file */
- errcode = -3;
- goto error;
- }
- qes_seq_fill_header(seq, seqfile->scratch.str, seqfile->scratch.len);
- /* Fill the actual sequence directly */
- len = qes_file_readline_str(seqfile->qf, &seq->seq);
- errcode = -4;
- CHECK_AND_TRIM(seq->seq)
- /* read the qual header, but don't store it. */
- errcode = -5;
- next = qes_file_getc(seqfile->qf);
- if (next != FASTQ_QUAL_DELIM) {
- goto error;
- }
- while ((next = qes_file_getc(seqfile->qf)) != '\n') {
- if (next == EOF) {
- goto error;
- }
- }
- if (next != '\n') goto error;
- /* Fill the qual score string directly */
- len = qes_file_readline_str(seqfile->qf, &seq->qual);
- errcode = -6;
- CHECK_AND_TRIM(seq->qual)
- if ((size_t)len != seq->seq.len) {
- /* Error out on different len qual/seq entries */
- errcode = -7;
- goto error;
- }
- /* return seq/qual len */
- seqfile->n_records++;
- return seq->seq.len;
-error:
- qes_str_nullify(&seq->name);
- qes_str_nullify(&seq->comment);
- qes_str_nullify(&seq->seq);
- qes_str_nullify(&seq->qual);
- return errcode;
-#undef CHECK_AND_TRIM
-}
-
-static inline ssize_t
-read_fasta_seqfile(struct qes_seqfile *seqfile, struct qes_seq *seq)
-{
- /* Convenience macro, this happens a lot */
-#define CHECK_AND_TRIM(subrec) if (len < 1) { \
- goto error; \
- } else { \
- subrec.str[--len] = '\0'; \
- subrec.len = len; \
- }
- ssize_t len = 0;
- int next = '\0';
-
- /* This bit is basically a copy-paste from above */
- /* Fast-forward past the delimiter '>', ensuring it exists */
- next = qes_file_getc(seqfile->qf);
- if (next == EOF) {
- return EOF;
- } else if (next != FASTA_DELIM) {
- /* This ain't a fasta! WTF! */
- goto error;
- }
- len = qes_file_readline_str(seqfile->qf, &seqfile->scratch);
- if (len < 1) {
- goto error;
- }
- qes_seq_fill_header(seq, seqfile->scratch.str, seqfile->scratch.len);
- /* we need to nullify seq, as we rely on seq.len being 0 as we enter this
- * while loop */
- qes_str_nullify(&seq->seq);
- qes_str_nullify(&seqfile->scratch);
- /* While the next char is not a '>', i.e. until next header line */
- while ((next = qes_file_peek(seqfile->qf)) != EOF && next != FASTA_DELIM) {
- len = qes_file_readline_str(seqfile->qf, &seqfile->scratch);
- CHECK_AND_TRIM(seqfile->scratch)
- if (len < 0) {
- goto error;
- }
- qes_str_cat(&seq->seq, &seqfile->scratch);
- }
- seq->seq.str[seq->seq.len] = '\0';
- /* return seq len */
- seqfile->n_records++;
- qes_str_nullify(&seq->qual);
- return seq->seq.len;
-error:
- qes_str_nullify(&seq->name);
- qes_str_nullify(&seq->comment);
- qes_str_nullify(&seq->seq);
- qes_str_nullify(&seq->qual);
- return -2;
-#undef CHECK_AND_TRIM
-}
-
-ssize_t
-qes_seqfile_read (struct qes_seqfile *seqfile, struct qes_seq *seq)
-{
- if (!qes_seqfile_ok(seqfile) || !qes_seq_ok(seq)) {
- return -2;
- }
- if (seqfile->qf->eof) {
- return EOF;
- }
- if (seqfile->format == FASTQ_FMT) {
- return read_fastq_seqfile(seqfile, seq);
- } else if (seqfile->format == FASTA_FMT) {
- return read_fasta_seqfile(seqfile, seq);
- }
- /* If we reach here, bail out with an error */
- qes_str_nullify(&seq->name);
- qes_str_nullify(&seq->comment);
- qes_str_nullify(&seq->seq);
- qes_str_nullify(&seq->qual);
- return -2;
-}
-
-struct qes_seqfile *
-qes_seqfile_create (const char *path, const char *mode)
-{
- struct qes_seqfile *sf = NULL;
- if (path == NULL || mode == NULL) return NULL;
- sf = qes_calloc(1, sizeof(*sf));
- sf->qf = qes_file_open(path, mode);
- if (sf->qf == NULL) {
- qes_free(sf->qf);
- qes_free(sf);
- return NULL;
- }
- qes_str_init(&sf->scratch, __INIT_LINE_LEN);
- sf->n_records = 0;
- qes_seqfile_guess_format(sf);
- return sf;
-}
-
-enum qes_seqfile_format
-qes_seqfile_guess_format (struct qes_seqfile *seqfile)
-{
- int first_char = '\0';
- if (!qes_seqfile_ok(seqfile)) return UNKNOWN_FMT;
- if (!qes_file_readable(seqfile->qf)) return UNKNOWN_FMT;
- first_char = qes_file_peek(seqfile->qf);
- switch (first_char) {
- case FASTQ_DELIM:
- seqfile->format = FASTQ_FMT;
- return FASTQ_FMT;
- break;
- case FASTA_DELIM:
- seqfile->format = FASTA_FMT;
- return FASTA_FMT;
- break;
- default:
- seqfile->format = UNKNOWN_FMT;
- return UNKNOWN_FMT;
- }
-}
-
-void
-qes_seqfile_set_format (struct qes_seqfile *seqfile,
- enum qes_seqfile_format format)
-{
- if (!qes_seqfile_ok(seqfile)) return;
- seqfile->format = format;
-}
-
-void
-qes_seqfile_destroy_(struct qes_seqfile *seqfile)
-{
- if (seqfile != NULL) {
- qes_file_close(seqfile->qf);
- qes_str_destroy_cp(&seqfile->scratch);
- qes_free(seqfile);
- }
-}
-
-size_t
-qes_seqfile_format_seq(const struct qes_seq *seq, enum qes_seqfile_format fmt,
- char *buffer, size_t maxlen)
-{
- size_t len = 0;
- if (buffer == NULL || maxlen < 1) {
- return 0;
- }
- switch (fmt) {
- case FASTQ_FMT:
- if (!qes_seq_ok(seq)) {
- buffer[0] = '\0';
- return 0;
- }
- len = snprintf(buffer, maxlen, "%c%s %s\n%s\n%c\n%s\n",
- FASTQ_DELIM, seq->name.str, seq->comment.str,
- seq->seq.str,
- FASTQ_QUAL_DELIM,
- seq->qual.str);
- return len;
- break;
- case FASTA_FMT:
- if (!qes_seq_ok_no_qual(seq)) {
- buffer[0] = '\0';
- return 0;
- }
- len = snprintf(buffer, maxlen, "%c%s %s\n%s\n",
- FASTA_DELIM, seq->name.str, seq->comment.str,
- seq->seq.str);
- return len;
- break;
- case UNKNOWN_FMT:
- default:
- return 0;
- }
-}
-
-
-ssize_t
-qes_seqfile_write (struct qes_seqfile *seqfile, struct qes_seq *seq)
-{
-#define sf_putc_check(c) ret = QES_ZFPUTC(seqfile->qf->fp, c); \
- if (ret != c) {return -2;} \
- else {res_len += 1;} \
- ret = 0
-#define sf_puts_check(s) ret = QES_ZFPUTS(seqfile->qf->fp, s.str); \
- if (ret < 0) {return -2;} \
- else {res_len += s.len;} \
- ret = 0
-
- int ret = 0;
- ssize_t res_len = 0;
-
- if (!qes_seqfile_ok(seqfile) || !qes_seq_ok(seq)) {
- return -2;
- }
- switch (seqfile->format) {
- case FASTA_FMT:
- sf_putc_check(FASTA_DELIM);
- sf_puts_check(seq->name);
- if (qes_seq_has_comment(seq)) {
- sf_putc_check(' ');
- sf_puts_check(seq->comment);
- }
- sf_putc_check('\n');
- sf_puts_check(seq->seq);
- sf_putc_check('\n');
- break;
- case FASTQ_FMT:
- sf_putc_check(FASTQ_DELIM);
- sf_puts_check(seq->name);
- if (qes_seq_has_comment(seq)) {
- sf_putc_check(' ');
- sf_puts_check(seq->comment);
- }
- sf_putc_check('\n');
- sf_puts_check(seq->seq);
- sf_putc_check('\n');
- if (qes_seq_has_qual(seq)) {
- sf_putc_check('+');
- sf_putc_check('\n');
- sf_puts_check(seq->qual);
- sf_putc_check('\n');
-
- }
- break;
- case UNKNOWN_FMT:
- default:
- return -2;
- break;
- }
- return res_len;
-#undef sf_putc_check
-#undef sf_puts_check
-}
diff --git a/src/libqes/src/qes_seqfile.h b/src/libqes/src/qes_seqfile.h
deleted file mode 100644
index ce69ad0..0000000
--- a/src/libqes/src/qes_seqfile.h
+++ /dev/null
@@ -1,240 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: qes_seqfile.h
- *
- * Description: qes_seqfile -- read sequences in FASTA or FASTQ format.
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#ifndef QES_SEQFILE_H
-#define QES_SEQFILE_H
-
-#include <qes_util.h>
-#include <qes_seq.h>
-#include <qes_file.h>
-
-
-/*--------------------------------------------------------------------------
- | Seqfile -- seamless reading & writing of FASTA & FASTQ |
- ---------------------------------------------------------------------------*/
-
-#define FASTA_DELIM '>'
-#define FASTQ_DELIM '@'
-#define FASTQ_QUAL_DELIM '+'
-
-enum qes_seqfile_format {
- UNKNOWN_FMT = 0,
- FASTA_FMT = 1,
- FASTQ_FMT = 2,
-};
-
-struct qes_seqfile {
- struct qes_file *qf;
- size_t n_records;
- enum qes_seqfile_format format;
- /* A buffer to store misc shit in while reading.
- One per file to keep it re-entrant */
- struct qes_str scratch;
-};
-
-
-/*=== FUNCTION ============================================================*
-Name: qes_seqfile_create
-Parameters: const char *path: Path to open.
- const char *mode: Mode to pass to the fopen equivalent used.
-Description: Allocates structures, initialises values and opens the internal
- file handle.
-Returns: A fully usable ``struct qes_seqfile *`` or NULL.
- *===========================================================================*/
-struct qes_seqfile *qes_seqfile_create (const char *path, const char *mode);
-
-
-/*=== FUNCTION ============================================================*
-Name: qes_seqfile_ok
-Parameters: const struct qes_seqfile *file: File reference to check.
-Description: Check a file reference ``file``, ensuring that it may be
- dereferenced and used. This checks if a buffer has been
- allocated and buffer pointers set appropriately IFF the file is
- opened for reading. No guarantees are given about being able to
- read from the file.
-Returns: An int evaluating to true if ``file`` is OK, otherwise false.
- *===========================================================================*/
-static inline int
-qes_seqfile_ok(const struct qes_seqfile *file)
-{
- return (file != NULL && qes_file_ok(file->qf));
-}
-
-
-
-/*=== FUNCTION ============================================================*
-Name: qes_seqfile_guess_format
-Parameters: struct qes_seqfile *file: File whose format we guess.
-Description: Guess, using qes_file_peek, the format of ``file``. This only inspects
- the first character, so it will be confused if the first
- character of the file is incorrect. Only use this at the start
- of a file (this is checked).
-Returns: The file's format as a enum qes_seqfile_format, or UNKNOWN_FMT if the
- file is not readable, or not a FASTA/FASTQ file.
- *===========================================================================*/
-enum qes_seqfile_format qes_seqfile_guess_format(struct qes_seqfile *file);
-
-void qes_seqfile_set_format (struct qes_seqfile *file,
- enum qes_seqfile_format format);
-
-ssize_t qes_seqfile_read (struct qes_seqfile *file, struct qes_seq *seq);
-
-ssize_t qes_seqfile_write (struct qes_seqfile *file, struct qes_seq *seq);
-
-size_t qes_seqfile_format_seq(const struct qes_seq *seq, enum qes_seqfile_format fmt,
- char *buffer, size_t maxlen);
-
-void qes_seqfile_destroy_(struct qes_seqfile *seqfile);
-#define qes_seqfile_destroy(seqfile) do { \
- qes_seqfile_destroy_(seqfile); \
- seqfile = NULL; \
- } while(0)
-
-#ifdef OPENMP_FOUND
-#define QES_SEQFILE_ITER_PARALLEL_SINGLE_BEGIN(fle, sq, ln, opts) \
- _Pragma(STRINGIFY(omp parallel shared(fle) opts default(none))) \
- { \
- struct qes_seq *sq = qes_seq_create(); \
- ssize_t ln = 0; \
- while(1) { \
- _Pragma(STRINGIFY(omp critical)) \
- { \
- ln = qes_seqfile_read(fle, sq); \
- } \
- if (ln < 0) { \
- break; \
- }
-
-#define QES_SEQFILE_ITER_PARALLEL_SINGLE_END(sq) \
- } \
- qes_seq_destroy(sq); \
- }
-
-#define QES_SEQFILE_ITER_PARALLEL_PAIRED_BEGIN(fle1, fle2, sq1, sq2, ln1, ln2, opts)\
- _Pragma(STRINGIFY(omp parallel shared(fle1, fle2) opts default(none))) \
- { \
- struct qes_seq *sq1 = qes_seq_create(); \
- struct qes_seq *sq2 = qes_seq_create(); \
- ssize_t ln1 = 0; \
- ssize_t ln2 = 0; \
- while(1) { \
- _Pragma(STRINGIFY(omp critical)) \
- { \
- ln1 = qes_seqfile_read(fle1, sq1); \
- ln2 = qes_seqfile_read(fle2, sq2); \
- } \
- if (ln1 < 0 || ln2 < 0) { \
- break; \
- }
-
-#define QES_SEQFILE_ITER_PARALLEL_PAIRED_END(sq1, sq2) \
- } \
- qes_seq_destroy(sq1); \
- qes_seq_destroy(sq2); \
- }
-
-#define QES_SEQFILE_ITER_PARALLEL_INTERLEAVED_BEGIN(fle, sq1, sq2, ln1, ln2, opts)\
- _Pragma(STRINGIFY(omp parallel shared(fle) opts default(none))) \
- { \
- struct qes_seq *sq1 = qes_seq_create(); \
- struct qes_seq *sq2 = qes_seq_create(); \
- ssize_t ln1 = 0; \
- ssize_t ln2 = 0; \
- while(1) { \
- _Pragma(STRINGIFY(omp critical)) \
- { \
- ln1 = qes_seqfile_read(fle, sq1); \
- ln2 = qes_seqfile_read(fle, sq2); \
- } \
- if (ln1 < 0 || ln2 < 0) { \
- break; \
- }
-
-#define QES_SEQFILE_ITER_PARALLEL_INTERLEAVED_END(sq1, sq2) \
- } \
- qes_seq_destroy(sq1); \
- qes_seq_destroy(sq2); \
- }
-
-#endif /* OPENMP_FOUND */
-
-#define QES_SEQFILE_ITER_SINGLE_BEGIN(fle, sq, ln) \
- { \
- struct qes_seq *sq = qes_seq_create(); \
- /* TODO MUSTFIX check for null sq */ \
- ssize_t ln = 0; \
- while(1) { \
- ln = qes_seqfile_read(fle, sq); \
- if (ln < 0) { \
- break; \
- }
-
-#define QES_SEQFILE_ITER_SINGLE_END(sq) \
- } \
- qes_seq_destroy(sq); \
- }
-
-#define QES_SEQFILE_ITER_PAIRED_BEGIN(fle1, fle2, sq1, sq2, ln1, ln2) \
- { \
- struct qes_seq *sq1 = qes_seq_create(); \
- struct qes_seq *sq2 = qes_seq_create(); \
- ssize_t ln1 = 0; \
- ssize_t ln2 = 0; \
- while(1) { \
- ln1 = qes_seqfile_read(fle1, sq1); \
- ln2 = qes_seqfile_read(fle2, sq2); \
- if (ln1 < 0 || ln2 < 0) { \
- break; \
- }
-
-#define QES_SEQFILE_ITER_PAIRED_END(sq1, sq2) \
- } \
- qes_seq_destroy(sq1); \
- qes_seq_destroy(sq2); \
- }
-
-#define QES_SEQFILE_ITER_INTERLEAVED_BEGIN(fle, sq1, sq2, ln1, ln2) \
- { \
- struct qes_seq *sq1 = qes_seq_create(); \
- struct qes_seq *sq2 = qes_seq_create(); \
- ssize_t ln1 = 0; \
- ssize_t ln2 = 0; \
- while(1) { \
- ln1 = qes_seqfile_read(fle, sq1); \
- ln2 = qes_seqfile_read(fle, sq2); \
- if (ln1 < 0 || ln2 < 0) { \
- break; \
- }
-
-#define QES_SEQFILE_ITER_INTERLEAVED_END(sq1, sq2) \
- } \
- qes_seq_destroy(sq1); \
- qes_seq_destroy(sq2); \
- }
-
-#endif /* QES_SEQFILE_H */
diff --git a/src/libqes/src/qes_sequtil.c b/src/libqes/src/qes_sequtil.c
deleted file mode 100644
index 124d44b..0000000
--- a/src/libqes/src/qes_sequtil.c
+++ /dev/null
@@ -1,272 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: qes_sequtil.c
- *
- * Description: Sequence utility functions
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "qes_sequtil.h"
-
-
-/*
- * === FUNCTION =============================================================
- * Name: qes_sequtil_translate_codon
- * Description: translate a codon to an amino acid.
- * ============================================================================
- */
-
-inline int
-qes_sequtil_translate_codon (const char *codon)
-{
- if (codon == NULL || strnlen(codon, 4) != 3) {
- return -1;
- }
- if (codon[0] == 'A') {
- if (codon[1] == 'A') {
- if (codon[2] == 'A') return 'K';
- else if (codon[2] == 'C') return 'N';
- else if (codon[2] == 'G') return 'K';
- else if (codon[2] == 'T') return 'N';
- else if (codon[2] == 'U') return 'N';
- }
- else if (codon[1] == 'C') {
- if (codon[2] == 'A') return 'T';
- else if (codon[2] == 'C') return 'T';
- else if (codon[2] == 'G') return 'T';
- else if (codon[2] == 'T') return 'T';
- else if (codon[2] == 'U') return 'T';
- }
- else if (codon[1] == 'G') {
- if (codon[2] == 'A') return 'R';
- else if (codon[2] == 'C') return 'S';
- else if (codon[2] == 'G') return 'R';
- else if (codon[2] == 'T') return 'S';
- else if (codon[2] == 'U') return 'S';
- }
- else if (codon[1] == 'T') {
- if (codon[2] == 'A') return 'I';
- else if (codon[2] == 'C') return 'I';
- else if (codon[2] == 'G') return 'M';
- else if (codon[2] == 'T') return 'I';
- else if (codon[2] == 'U') return 'I';
- }
- else if (codon[1] == 'U') {
- if (codon[2] == 'A') return 'I';
- else if (codon[2] == 'C') return 'I';
- else if (codon[2] == 'G') return 'M';
- else if (codon[2] == 'T') return 'I';
- else if (codon[2] == 'U') return 'I';
- }
- }
- else if (codon[0] == 'C') {
- if (codon[1] == 'A') {
- if (codon[2] == 'A') return 'Q';
- else if (codon[2] == 'C') return 'H';
- else if (codon[2] == 'G') return 'Q';
- else if (codon[2] == 'T') return 'H';
- else if (codon[2] == 'U') return 'H';
- }
- else if (codon[1] == 'C') {
- if (codon[2] == 'A') return 'P';
- else if (codon[2] == 'C') return 'P';
- else if (codon[2] == 'G') return 'P';
- else if (codon[2] == 'T') return 'P';
- else if (codon[2] == 'U') return 'P';
- }
- else if (codon[1] == 'G') {
- if (codon[2] == 'A') return 'R';
- else if (codon[2] == 'C') return 'R';
- else if (codon[2] == 'G') return 'R';
- else if (codon[2] == 'T') return 'R';
- else if (codon[2] == 'U') return 'R';
- }
- else if (codon[1] == 'T') {
- if (codon[2] == 'A') return 'L';
- else if (codon[2] == 'C') return 'L';
- else if (codon[2] == 'G') return 'L';
- else if (codon[2] == 'T') return 'L';
- else if (codon[2] == 'U') return 'L';
- }
- else if (codon[1] == 'U') {
- if (codon[2] == 'A') return 'L';
- else if (codon[2] == 'C') return 'L';
- else if (codon[2] == 'G') return 'L';
- else if (codon[2] == 'T') return 'L';
- else if (codon[2] == 'U') return 'L';
- }
- }
- else if (codon[0] == 'G') {
- if (codon[1] == 'A') {
- if (codon[2] == 'A') return 'E';
- else if (codon[2] == 'C') return 'D';
- else if (codon[2] == 'G') return 'E';
- else if (codon[2] == 'T') return 'D';
- else if (codon[2] == 'U') return 'D';
- }
- else if (codon[1] == 'C') {
- if (codon[2] == 'A') return 'A';
- else if (codon[2] == 'C') return 'A';
- else if (codon[2] == 'G') return 'A';
- else if (codon[2] == 'T') return 'A';
- else if (codon[2] == 'U') return 'A';
- }
- else if (codon[1] == 'G') {
- if (codon[2] == 'A') return 'G';
- else if (codon[2] == 'C') return 'G';
- else if (codon[2] == 'G') return 'G';
- else if (codon[2] == 'T') return 'G';
- else if (codon[2] == 'U') return 'G';
- }
- else if (codon[1] == 'T') {
- if (codon[2] == 'A') return 'V';
- else if (codon[2] == 'C') return 'V';
- else if (codon[2] == 'G') return 'V';
- else if (codon[2] == 'T') return 'V';
- else if (codon[2] == 'U') return 'V';
- }
- else if (codon[1] == 'U') {
- if (codon[2] == 'A') return 'V';
- else if (codon[2] == 'C') return 'V';
- else if (codon[2] == 'G') return 'V';
- else if (codon[2] == 'T') return 'V';
- else if (codon[2] == 'U') return 'V';
- }
- }
- else if (codon[0] == 'T') {
- if (codon[1] == 'A') {
- if (codon[2] == 'A') return '*';
- else if (codon[2] == 'C') return 'Y';
- else if (codon[2] == 'G') return '*';
- else if (codon[2] == 'T') return 'Y';
- else if (codon[2] == 'U') return 'Y';
- }
- else if (codon[1] == 'C') {
- if (codon[2] == 'A') return 'S';
- else if (codon[2] == 'C') return 'S';
- else if (codon[2] == 'G') return 'S';
- else if (codon[2] == 'T') return 'S';
- else if (codon[2] == 'U') return 'S';
- }
- else if (codon[1] == 'G') {
- if (codon[2] == 'A') return '*';
- else if (codon[2] == 'C') return 'C';
- else if (codon[2] == 'G') return 'W';
- else if (codon[2] == 'T') return 'C';
- else if (codon[2] == 'U') return 'C';
- }
- else if (codon[1] == 'T') {
- if (codon[2] == 'A') return 'L';
- else if (codon[2] == 'C') return 'F';
- else if (codon[2] == 'G') return 'L';
- else if (codon[2] == 'T') return 'F';
- else if (codon[2] == 'U') return 'F';
- }
- else if (codon[1] == 'U') {
- if (codon[2] == 'A') return 'L';
- else if (codon[2] == 'C') return 'F';
- else if (codon[2] == 'G') return 'L';
- else if (codon[2] == 'T') return 'F';
- else if (codon[2] == 'U') return 'F';
- }
- }
- else if (codon[0] == 'U') {
- if (codon[1] == 'A') {
- if (codon[2] == 'A') return '*';
- else if (codon[2] == 'C') return 'Y';
- else if (codon[2] == 'G') return '*';
- else if (codon[2] == 'T') return 'Y';
- else if (codon[2] == 'U') return 'Y';
- }
- else if (codon[1] == 'C') {
- if (codon[2] == 'A') return 'S';
- else if (codon[2] == 'C') return 'S';
- else if (codon[2] == 'G') return 'S';
- else if (codon[2] == 'T') return 'S';
- else if (codon[2] == 'U') return 'S';
- }
- else if (codon[1] == 'G') {
- if (codon[2] == 'A') return '*';
- else if (codon[2] == 'C') return 'C';
- else if (codon[2] == 'G') return 'W';
- else if (codon[2] == 'T') return 'C';
- else if (codon[2] == 'U') return 'C';
- }
- else if (codon[1] == 'T') {
- if (codon[2] == 'A') return 'L';
- else if (codon[2] == 'C') return 'F';
- else if (codon[2] == 'G') return 'L';
- else if (codon[2] == 'T') return 'F';
- else if (codon[2] == 'U') return 'F';
- }
- else if (codon[1] == 'U') {
- if (codon[2] == 'A') return 'L';
- else if (codon[2] == 'C') return 'F';
- else if (codon[2] == 'G') return 'L';
- else if (codon[2] == 'T') return 'F';
- else if (codon[2] == 'U') return 'F';
- }
- }
- return 'X';
-}
-
-
-inline char *
-qes_sequtil_revcomp (const char *seq, size_t len)
-{
- size_t seqlen = strlen(seq);
- char *outseq = strdup(seq);
- seqlen = seqlen < len ? seqlen : len - 1;
-
- if (outseq[seqlen - 1] == '\n') {
- outseq[seqlen - 1] = '\0';
- seqlen--;
- }
-
- qes_sequtil_revcomp_inplace(outseq, len);
- return outseq;
-}
-
-inline void
-qes_sequtil_revcomp_inplace (char *seq, size_t len)
-{
- size_t iii;
- /* Trim trailing whitespace */
- while (len > 0 && isspace(seq[len - 1])) {
- seq[--len] = '\0';
- }
- for (iii = 0; iii < len && seq[iii] != '\0'; iii++) {
- size_t endpos = len - iii - 1;
- char endchar = seq[endpos];
- if (seq[iii] == 'a' || seq[iii] == 'A') seq[endpos] = 'T';
- else if (seq[iii] == 'c' || seq[iii] == 'C') seq[endpos] = 'G';
- else if (seq[iii] == 'g' || seq[iii] == 'G') seq[endpos] = 'C';
- else if (seq[iii] == 't' || seq[iii] == 'T') seq[endpos] = 'A';
- else seq[endpos] = 'N';
- if (endchar == 'a' || endchar == 'A') seq[iii] = 'T';
- else if (endchar == 'c' || endchar == 'C') seq[iii] = 'G';
- else if (endchar == 'g' || endchar == 'G') seq[iii] = 'C';
- else if (endchar == 't' || endchar == 'T') seq[iii] = 'A';
- else seq[iii] = 'N';
- }
-}
diff --git a/src/libqes/src/qes_sequtil.h b/src/libqes/src/qes_sequtil.h
deleted file mode 100644
index f3369b9..0000000
--- a/src/libqes/src/qes_sequtil.h
+++ /dev/null
@@ -1,39 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: qes_sequtil.h
- *
- * Description: Sequence utility functions
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#ifndef QES_SEQUTIL_H
-#define QES_SEQUTIL_H
-
-#include <qes_util.h>
-
-
-extern int qes_sequtil_translate_codon(const char *codon);
-extern char *qes_sequtil_revcomp(const char *seq, size_t len);
-extern void qes_sequtil_revcomp_inplace(char *seq, size_t len);
-
-#endif /* QES_SEQUTIL_H */
diff --git a/src/libqes/src/qes_str.c b/src/libqes/src/qes_str.c
deleted file mode 100644
index 6f173a1..0000000
--- a/src/libqes/src/qes_str.c
+++ /dev/null
@@ -1,52 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: qes_str.c
- *
- * Description: String handling functions
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "qes_str.h"
-
-
-void
-qes_str_print (const struct qes_str *str, FILE *stream)
-{
- if (qes_str_ok(str)) {
- fwrite(str->str, 1, str->len, stream);
- }
-}
-
-void
-qes_str_destroy_cp (struct qes_str *str)
-{
- if (str != NULL) qes_free(str->str);
-}
-
-void
-qes_str_destroy (struct qes_str *str)
-{
- qes_str_destroy_cp(str);
- qes_free(str);
-}
-
diff --git a/src/libqes/src/qes_str.h b/src/libqes/src/qes_str.h
deleted file mode 100644
index 79fed96..0000000
--- a/src/libqes/src/qes_str.h
+++ /dev/null
@@ -1,184 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: qes_str.h
- *
- * Description: String handling functions
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#ifndef QES_STR_H
-#define QES_STR_H
-
-#include <qes_util.h>
-
-struct qes_str {
- char *str;
- size_t len;
- size_t capacity;
-};
-
-
-/*=== FUNCTION ============================================================*
-Name: qes_str_ok
-Parameters: const struct qes_str *str: `struct qes_str` ref to check.
-Description: Checks if a string is OK to use, i.e. checks that `str->str` is
- a valid `char` array.
-Returns: An `int` that evaluates to true or false.
- *===========================================================================*/
-static inline int
-qes_str_ok (const struct qes_str *str)
-{
- return str != NULL && str->str != NULL && str->capacity > 0;
-}
-
-/*=== FUNCTION ============================================================*
-Name: qes_str_init
-Parameters: struct qes_str *str: String to initialise (normally on the
- stack).
- size_t len: Initial capacity of `struct qes_str`.
-Description: Initialise a `struct qes_str` (typically on the stack) with
- room for `len` characters.
-Returns: void
- *===========================================================================*/
-static inline void
-qes_str_init (struct qes_str *str, size_t capacity)
-{
- if (str == NULL) return;
- str->len = 0;
- str->str = qes_calloc(capacity, sizeof(*str->str));
- str->capacity = capacity;
-}
-
-/*=== FUNCTION ============================================================*
-Name: qes_str_create
-Parameters: size_t len: Initial capacity of `struct qes_str`.
-Description: Create a `struct qes_str` on the heap with room for `len`
- characters.
-Returns: `struct qes_str *` Pointer to a memory address.
- *===========================================================================*/
-static inline struct qes_str *
-qes_str_create (size_t capacity)
-{
- struct qes_str *str = qes_calloc(1, sizeof(*str));
-
- /* We don't worry about NULL here. qes_str_init will return before
- * derefencing and we'll return NULL below. */
- qes_str_init(str, capacity);
- return str;
-}
-
-static inline int
-qes_str_resize (struct qes_str *str, size_t len)
-{
- if (str == NULL) return 0;
- if (str->capacity < len + 1) {
- while (str->capacity < len + 1) {
- str->capacity = qes_roundupz(str->capacity);
- }
- str->str = qes_realloc(str->str, str->capacity * sizeof(*str->str));
- }
- return 1;
-}
-
-static inline int
-qes_str_fill_charptr (struct qes_str *str, const char *cp, size_t len)
-{
- if (str == NULL || cp == NULL) return 0;
- if (len == 0) {
- len = strlen(cp);
- }
- qes_str_resize(str, len);
- memcpy(str->str, cp, len);
- str->str[len] = '\0';
- str->len = len;
- return 1;
-}
-
-/*=== FUNCTION ============================================================*
-Name: qes_str_nullify
-Parameters: struct qes_str *str: `struct qes_str` to nullify.
-Description: Invalidates a `struct qes_str` without freeing the `char []`.
-Returns: int: 0 on success, otherwise 1.
- *===========================================================================*/
-static inline int
-qes_str_nullify (struct qes_str *str)
-{
- if (!qes_str_ok(str)) return 1;
- str->str[0] = '\0';
- str->len = 0;
- return 0;
-}
-
-static inline int
-qes_str_copy (struct qes_str *dest, const struct qes_str *src)
-{
- if (!qes_str_ok(src) || dest == NULL) return 1;
- if (!qes_str_ok(dest)) qes_str_init(dest, src->capacity);
- else qes_str_resize(dest, src->capacity);
- memcpy(dest->str, src->str, src->capacity);
- return 0;
-}
-
-static inline int
-qes_str_cat (struct qes_str *dest, const struct qes_str *src)
-{
- if (!qes_str_ok(src) || dest == NULL) return 1;
- if (!qes_str_ok(dest)) qes_str_init(dest, src->capacity);
- else qes_str_resize(dest, dest->len + src->len);
-
- memcpy(dest->str + dest->len, src->str, src->len);
- dest->len += src->len;
- dest->str[dest->len] = '\0';
- return 0;
-}
-
-static inline int
-qes_str_truncate (struct qes_str *str, const size_t at)
-{
- if (!qes_str_ok(str)) return 1;
- if (at >= str->len) return 0;
- str->str[at] = '\0';
- str->len = at;
- return 0;
-}
-
-extern void qes_str_print (const struct qes_str *str, FILE *stream);
-
-/*=== FUNCTION ============================================================*
-Name: qes_str_destroy
-Parameters: struct qes_str *: `struct qes_str` to destroy.
-Description: Frees `str->str` and the struct qes_str struct itself.
-Returns: void
- *===========================================================================*/
-extern void qes_str_destroy (struct qes_str *str);
-
-/*=== FUNCTION ============================================================*
-Name: qes_str_destroy_cp
-Parameters: struct qes_str *: String to destrop
-Description: Frees `str->str` without freeing the struct qes_str struct
- itself. For use on `struct qes_str`s allocated on the stack.
-Returns: void
- *===========================================================================*/
-extern void qes_str_destroy_cp (struct qes_str *str);
-
-#endif /* QES_STR_H */
diff --git a/src/libqes/src/qes_util.c b/src/libqes/src/qes_util.c
deleted file mode 100644
index 1586fac..0000000
--- a/src/libqes/src/qes_util.c
+++ /dev/null
@@ -1,75 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: qes_util.c
- *
- * Description: Wrappers around std library functions
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "qes_util.h"
-
-
-/* Pull LIBQES_VERSION in from qes_config.h */
-const char *libqes_version = LIBQES_VERSION;
-
-/* Valid non-function to pass to libqes functions */
-void
-errnil (QES_ERRFN_ARGS)
-{
- (void) (msg);
- (void) (file);
- (void) (line);
-}
-
-/* Function to pass to libqes functions which prints out errors to stderr */
-void
-errprint (QES_ERRFN_ARGS)
-{
- char msg_fmt[1<<8] = "";
- va_list args;
- if (msg == NULL) {
- msg = "GENERIC ERROR WITH NO MESSAGE";
- }
- va_start (args, line);
- vsnprintf(msg_fmt, 1<<8, msg, args);
- va_end (args);
- fprintf(stderr, "[%s: %d]: %s\n", file, line, msg_fmt);
-}
-
-/* Function to pass to libqes functions which prints out errors to stderr and
- calls `exit(EXIT_FAILURE)` */
-void
-errprintexit (QES_ERRFN_ARGS)
-{
- char msg_fmt[1<<8] = "";
- va_list args;
- if (msg == NULL) {
- msg = "GENERIC ERROR WITH NO MESSAGE";
- }
- va_start (args, line);
- vsnprintf(msg_fmt, 1<<8, msg, args);
- va_end (args);
- fprintf(stderr, "[%s: %d]: %s\n", file, line, msg_fmt);
- QES_EXIT_FN(EXIT_FAILURE);
-}
-
diff --git a/src/libqes/src/qes_util.h b/src/libqes/src/qes_util.h
deleted file mode 100644
index 8e01ce1..0000000
--- a/src/libqes/src/qes_util.h
+++ /dev/null
@@ -1,250 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- ============================================================================
- *
- * Filename: qes_util.h
- *
- * Description: Wrappers around std library functions
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#ifndef QES_UTIL_H
-#define QES_UTIL_H
-
-
-/* ##### HEADER FILE INCLUDES ########################################## */
-#include <ctype.h>
-#include <errno.h>
-#include <stdarg.h>
-#include <stddef.h>
-#include <stdint.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <strings.h>
-#include "qes_config.h"
-
-
-/*
- * Cross-platform bollocks. Thanks windows.
- */
-
-#if defined(WIN32) || defined(_WIN32)
-#include <windows.h>
-#define QES_PATHSEP "\\"
-#else
-#define QES_PATHSEP "/"
-#include <unistd.h>
-#endif
-
-/*
- * Misc constants
- */
-
-extern const char *libqes_version;
-
-#define QES_MAX_FN_LEN (1<<16)
-/* Size of buffers for file IO */
-#define QES_FILEBUFFER_LEN (16384)
-/* Starting point for allocing a char pointer. Set to slightly larger than the
- standard size of whatever you're reading in. */
-#define __INIT_LINE_LEN (128)
-
-/*
- * Macro helpers from tor
- */
-
-/* Expands to a syntactically valid empty statement. */
-#define STMT_NIL (void)0
-
-/* Expands to a syntactically valid empty statement, explicitly (void)ing its
- * argument. */
-#define STMT_VOID(a) while (0) { (void)(a); }
-
-/* STMT_BEGIN and STMT_END are used to wrap blocks inside macros so that
- * the macro can be used as if it were a single C statement. */
-#ifdef __GNUC__
- #define STMT_BEGIN (void) __extension__ ({
- #define STMT_END })
-#elif defined(sun) || defined(__sun__)
- #define STMT_BEGIN if (1) {
- #define STMT_END } else STMT_NIL
-#else
- #define STMT_BEGIN do {
- #define STMT_END } while (0)
-#endif
-
-/* This can be helpful in some macros, particularly with #pragma */
-#ifndef STRINGIFY
- #define STRINGIFY(a) #a
-#endif
-
-/*
- * Error handling functions
- */
-
-/* use the stdlib exit function by default, during testing we can #define this
- * to some kind of error handler if we need to. */
-#ifndef QES_EXIT_FN
- #define QES_EXIT_FN exit
-#endif
-
-
-/* By default, we use this error handler. At compile or include time, we can
- * chose another more appropriate one if we need to. */
-#ifndef QES_DEFAULT_ERR_FN
- #define QES_DEFAULT_ERR_FN errprintexit
-#endif
-
-
-#define QES_ERRFN_ARGS const char *msg, const char *file, int line, ...
-void errnil(QES_ERRFN_ARGS);
-void errprint (QES_ERRFN_ARGS);
-void errprintexit (QES_ERRFN_ARGS) __attribute__ ((noreturn));
-typedef void (*qes_errhandler_func) (const char*, const char *, int, ...);
-
-/* qes_roundupz:
- * Round up a `size_t` to the next highest power of two.
- */
-/* Flogged from http://stackoverflow.com/a/1322548 and
- http://graphics.stanford.edu/~seander/bithacks.html, and kseq.h */
-static inline size_t
-qes_roundupz (size_t sz)
-{
- /* Decrement v only if v is not already a power of 2 */
- /* I.e, roundup things already a power of 2 */
- if ((sz & (sz - 1)) != 0) sz--;
- /* mask all bits below MSB to 1 */
- sz |= sz>>1;
- sz |= sz>>2;
- sz |= sz>>4;
- sz |= sz>>8;
- sz |= sz>>16;
-#if UINTPTR_MAX == 0xffffffffffffffff /* 64-bit system */
- sz |= sz>>32;
-#endif
- return sz + 1;
-}
-
-static inline uint32_t
-qes_roundup32 (uint32_t u32)
-{
- /* Roundup things already a power of 2 */
- if ((u32 & (u32 - 1)) != 0) u32--;
- /* mask all bits below MSB to 1 */
- u32 |= u32>>1;
- u32 |= u32>>2;
- u32 |= u32>>4;
- u32 |= u32>>8;
- u32 |= u32>>16;
- return u32 + 1;
-}
-
-static inline uint64_t
-qes_roundup64 (uint64_t u64)
-{
- /* Roundup things already a power of 2 */
- if ((u64 & (u64 - 1)) != 0) u64--;
- /* mask all bits below MSB to 1 */
- u64 |= u64>>1;
- u64 |= u64>>2;
- u64 |= u64>>4;
- u64 |= u64>>8;
- u64 |= u64>>16;
- u64 |= u64>>32;
- return u64 + 1;
-}
-
-
-/* INLINE FUNCTIONS */
-
-/* Memory allocation/deallocation */
-static inline void *
-qes_calloc_ (size_t n, size_t size, qes_errhandler_func onerr, const char *file,
- int line)
-{
- void *ret = calloc(n, size);
- if (ret == NULL) {
- (*onerr)("calloc returned NULL -- Out of memory", file, line);
- return NULL;
- } else {
- return ret;
- }
-}
-#define qes_calloc(n, sz) \
- qes_calloc_(n, sz, QES_DEFAULT_ERR_FN, __FILE__, __LINE__)
-#define qes_calloc_errnil(n, sz) \
- qes_calloc_(n, sz, errnil, __FILE__, __LINE__)
-#define qes_calloc_errprint(n, sz) \
- qes_calloc_(n, sz, errprint, __FILE__, __LINE__)
-#define qes_calloc_errprintexit(n, sz) \
- qes_calloc_(n, sz, errprintexit, __FILE__, __LINE__)
-
-static inline void *
-qes_malloc_ (size_t size, qes_errhandler_func onerr, const char *file, int line)
-{
- void *ret = malloc(size);
- if (ret == NULL) {
- (*onerr)("malloc returned NULL -- Out of memory", file, line);
- return NULL;
- } else {
- return ret;
- }
-}
-#define qes_malloc(sz) \
- qes_malloc_(sz, QES_DEFAULT_ERR_FN, __FILE__, __LINE__)
-#define qes_malloc_errnil(sz) \
- qes_malloc_(sz, errnil, __FILE__, __LINE__)
-#define qes_malloc_errprint(sz) \
- qes_malloc_(sz, errprint, __FILE__, __LINE__)
-#define qes_malloc_errprintexit(sz) \
- qes_malloc_(sz, errprintexit, __FILE__, __LINE__)
-
-static inline void *
-qes_realloc_ (void *data, size_t size, qes_errhandler_func onerr, const char *file,
- int line)
-{
- void *ret = realloc(data, size);
- if (ret == NULL) {
- (*onerr)("realloc returned NULL -- Out of memory", file, line);
- return NULL;
- } else {
- return ret;
- }
-}
-
-#define qes_realloc(ptr, sz) \
- qes_realloc_(ptr, sz, QES_DEFAULT_ERR_FN, __FILE__, __LINE__)
-#define qes_realloc_errnil(ptr, sz) \
- qes_realloc_(ptr, sz, errnil, __FILE__, __LINE__)
-#define qes_realloc_errprint(ptr, sz) \
- qes_realloc_(ptr, sz, errprint, __FILE__, __LINE__)
-#define qes_realloc_errprintexit(ptr, sz) \
- qes_realloc_(ptr, sz, errprintexit, __FILE__, __LINE__)
-#define qes_free(data) \
- STMT_BEGIN \
- if (data != NULL) { \
- free(data); \
- data = NULL; \
- } \
- STMT_END
-
-#endif /* QES_UTIL_H */
diff --git a/src/libqes/test/CMakeLists.txt b/src/libqes/test/CMakeLists.txt
deleted file mode 100644
index 845853d..0000000
--- a/src/libqes/test/CMakeLists.txt
+++ /dev/null
@@ -1,45 +0,0 @@
-## Compile tests, & set up coverage
-SET(COMMON_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/helpers.c)
-FILE(GLOB TEST_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/test*.c)
-SET(TEST_SRCS ${COMMON_SRCS} ${TEST_SRCS} ${CMAKE_CURRENT_SOURCE_DIR}/tinytest/tinytest.c)
-ADD_EXECUTABLE(test_libqes ${TEST_SRCS})
-TARGET_LINK_LIBRARIES(test_libqes qes ${LIBQES_DEPENDS_LIBS})
-IF (CMAKE_BUILD_TYPE STREQUAL "Coverage")
- SETUP_TARGET_FOR_COVERAGE(coverage test_libqes coverage src)
-ENDIF()
-ADD_TEST(NAME run_test_libqes
- COMMAND ${CMAKE_BINARY_DIR}/bin/test_libqes ${CMAKE_BINARY_DIR})
-
-ADD_EXECUTABLE(qes_seqcat ${CMAKE_CURRENT_SOURCE_DIR}/qes_seqcat.c)
-TARGET_LINK_LIBRARIES(qes_seqcat qes ${LIBQES_DEPENDS_LIBS})
-
-ADD_EXECUTABLE(qes_seqprint ${CMAKE_CURRENT_SOURCE_DIR}/qes_seqprint.c)
-TARGET_LINK_LIBRARIES(qes_seqprint qes ${LIBQES_DEPENDS_LIBS})
-
-ADD_EXECUTABLE(kseqcat ${CMAKE_CURRENT_SOURCE_DIR}/kseqcat.c)
-TARGET_LINK_LIBRARIES(kseqcat qes ${LIBQES_DEPENDS_LIBS})
-
-# Demos
-ADD_EXECUTABLE(log_demo ${CMAKE_CURRENT_SOURCE_DIR}/logdemo.c)
-TARGET_LINK_LIBRARIES(log_demo qes ${LIBQES_DEPENDS_LIBS})
-ADD_TEST(NAME run_log_demo
- COMMAND ${CMAKE_BINARY_DIR}/bin/log_demo)
-
-# Benchmarking:
-ADD_EXECUTABLE(bench_libqes ${CMAKE_CURRENT_SOURCE_DIR}/benchmarks.c ${COMMON_SRCS})
-TARGET_LINK_LIBRARIES(bench_libqes qes ${LIBQES_DEPENDS_LIBS})
-ADD_TEST(NAME run_bench_libqes
- COMMAND ${CMAKE_BINARY_DIR}/bin/bench_libqes
- ${CMAKE_BINARY_DIR}/data/test.fastq
- 50
- qes_seqfile_write
- kseq_parse_fq
- gnu_getline
- qes_seqfile_parse_fq
- qes_file_readline_realloc)
-
-# Copy test files over to bin dir
-ADD_CUSTOM_COMMAND(TARGET test_libqes
- COMMAND ${CMAKE_COMMAND} -E copy_directory
- ${CMAKE_CURRENT_SOURCE_DIR}/data
- ${CMAKE_BINARY_DIR}/data)
diff --git a/src/libqes/test/benchmarks.c b/src/libqes/test/benchmarks.c
deleted file mode 100644
index ec36dc3..0000000
--- a/src/libqes/test/benchmarks.c
+++ /dev/null
@@ -1,311 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: benchmarks.c
- *
- * Description: Some benchmarks
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include <assert.h>
-#include <stdlib.h>
-#include <time.h>
-#include <stdlib.h>
-#include <qes_file.h>
-#include <qes_seqfile.h>
-#ifdef ZLIB_FOUND
-# include <zlib.h>
-#else
-# include <sys/stat.h>
-# include <fcntl.h>
-#endif
-
-#include "helpers.h"
-#include "kseq.h"
-
-
-void bench_qes_file_readline_realloc_file(int silent);
-void bench_qes_file_readline_file(int silent);
-#ifdef GELINE_FOUND
-void bench_gnu_getline_file(int silent);
-#endif
-void bench_qes_seqfile_parse_fq(int silent);
-void bench_kseq_parse_fq(int silent);
-void bench_qes_seqfile_write(int silent);
-#ifdef OPENMP_FOUND
-void bench_qes_seqfile_par_iter_fq_macro(int silent);
-#endif
-
-
-#ifdef ZLIB_FOUND
-KSEQ_INIT(gzFile, gzread)
-#else
-KSEQ_INIT(int, read)
-#endif
-
-static char *infile;
-
-typedef struct __bench {
- const char *name;
- void (*fn)(int silent);
-} bench_t;
-
-void
-bench_qes_file_readline_realloc_file(int silent)
-{
- size_t bsz = 1<<4;
- char *buf = malloc(bsz);
- ssize_t len = 0;
- off_t flen = 0;
- struct qes_file *file = qes_file_open(infile, "r");
-
- assert(buf != NULL);
- while ((len = qes_file_readline_realloc(file, &buf, &bsz)) != EOF) {
- flen += len;
- }
- if (!silent)
- printf("[qes_file_readline_realloc]\tFile of %lu chars\n",
- (long unsigned)flen);
- qes_file_close(file);
- free(buf);
-}
-
-void
-bench_qes_file_readline_file(int silent)
-{
- size_t bsz = 1<<10;
- char buf[bsz];
- ssize_t len = 0;
- off_t flen = 0;
-
- struct qes_file *file = qes_file_open(infile, "r");
- while ((len = qes_file_readline(file, buf, bsz)) != EOF) {
- flen += len;
- }
- if (!silent)
- printf("[qes_file_readline]\t\tFile of %lu chars\n",
- (long unsigned)flen);
- qes_file_close(file);
-}
-
-#ifdef GELINE_FOUND
-void
-bench_gnu_getline_file(int silent)
-{
- size_t bsz = 1<<4;
- char *buf = malloc(bsz);
- ssize_t len = 0;
- off_t flen = 0;
- FILE *file = fopen(infile, "r");
-
- assert(buf != NULL);
- while ((len = getline(&buf, &bsz, file)) != EOF) {
- flen += len;
- }
- if (!silent)
- printf("[getline]\t\tFile of %lu chars\n",
- (long unsigned)flen);
- fclose(file);
- free(buf);
-}
-#endif
-
-
-#ifdef OPENMP_FOUND
-void
-bench_qes_seqfile_par_iter_fq_macro(int silent)
-{
- struct qes_seqfile *sf = qes_seqfile_create(infile, "r");
- size_t total_len = 0;
-
- QES_SEQFILE_ITER_PARALLEL_SINGLE_BEGIN(sf, seq, seq_len, shared(total_len))
- #pragma omp critical
- {
- total_len += seq->seq.len;
- }
- QES_SEQFILE_ITER_PARALLEL_SINGLE_END(seq)
-
- if (!silent) {
- printf("[qes_seqfile_iter_fq_macro] Total seq len %lu\n",
- (long unsigned)total_len);
- }
- qes_seqfile_destroy(sf);
-}
-#endif
-
-void
-bench_qes_seqfile_parse_fq(int silent)
-{
- struct qes_seq *seq = qes_seq_create();
- struct qes_seqfile *sf = qes_seqfile_create(infile, "r");
- ssize_t res = 0;
- size_t n_recs = 0;
- size_t seq_len = 0;
-
- while (res != EOF) {
- res = qes_seqfile_read(sf, seq);
- if (res < 1) {
- break;
- }
- seq_len += res;
- n_recs++;
- }
- if (!silent) {
- printf("[qes_seqfile_fq] Total seq len %lu\n",
- (long unsigned)seq_len);
- }
- qes_seqfile_destroy(sf);
- qes_seq_destroy(seq);
-}
-
-void
-bench_kseq_parse_fq(int silent)
-{
-#ifdef ZLIB_FOUND
- gzFile fp = gzopen(infile, "r");
-#else
- int fp = open(infile, O_RDONLY);
-#endif
- kseq_t *seq = kseq_init(fp);
- ssize_t res = 0;
- size_t n_recs = 0;
- size_t seq_len = 0;
-
- while ((res = kseq_read(seq)) >= 0) {
- seq_len += res;
- n_recs++;
- }
- if (!silent) {
- printf("[kseq_fq] Total seq len %lu\n",
- (long unsigned) seq_len);
- }
- kseq_destroy(seq);
-#ifdef ZLIB_FOUND
- gzclose(fp);
-#else
- close(fp);
-#endif
-}
-
-void
-bench_qes_seqfile_write(int silent)
-{
- struct qes_seq *seq = qes_seq_create();
- ssize_t res = 0;
- struct qes_seqfile *sf = NULL;
- char *fname = tmpnam(NULL);
- size_t iii = 0;
-
- /* Make a seq to write */
- qes_seq_fill_name(seq, "HWI-TEST", 8);
- qes_seq_fill_comment(seq, "testseq 1 2 3", 13);
- qes_seq_fill_seq(seq, "ACTCAATT", 8);
- qes_seq_fill_qual(seq, "IIIIIIII", 8);
- /* Setup file for writing */
- sf = qes_seqfile_create(fname, "wT");
- qes_seqfile_set_format(sf, FASTQ_FMT);
- for (iii = 0; iii < 1<<11; iii++) {
- res += qes_seqfile_write(sf, seq);
- }
- if (!silent) {
- printf("[qes_seqfile_write] Total file len %lu to %s\n",
- (long unsigned)res, fname);
- }
- qes_seqfile_destroy(sf);
- qes_seq_destroy(seq);
- remove(fname);
-
-}
-
-static const bench_t benchmarks[] = {
- { "qes_file_readline", &bench_qes_file_readline_file},
- { "qes_file_readline_realloc", &bench_qes_file_readline_realloc_file},
-#ifdef GELINE_FOUND
- { "gnu_getline", &bench_gnu_getline_file},
-#endif
- { "qes_seqfile_parse_fq", &bench_qes_seqfile_parse_fq},
-#ifdef OPENMP_FOUND
- { "qes_seqfile_par_iter_fq_macro", &bench_qes_seqfile_par_iter_fq_macro},
-#endif
- { "kseq_parse_fq", &bench_kseq_parse_fq},
- { "qes_seqfile_write", &bench_qes_seqfile_write},
- { NULL, NULL}
-};
-
-int
-main (int argc, char *argv[])
-{
- bench_t thisbench;
- clock_t start, end;
- size_t iii = 0;
- int rnds = 0;
- size_t nbench = 0;
-
- if (argc == 1) {
- fprintf(stderr, "USAGE:\nbench <file> <rounds> <bench> [<bench> ...]\n\n");
- fprintf(stderr, "\nAvalilable benchmarks are:\n");
- nbench = 0;
- while (1) {
- thisbench = benchmarks[nbench++];
- if ((thisbench.name && thisbench.fn)) {
- fprintf(stderr, "%s\n", thisbench.name);
- } else {
- return EXIT_FAILURE;
- }
- }
- }
- if (argc < 4) {
- fprintf(stderr, "USAGE:\nbench <file> <rounds> <bench> [<bench> ...]\n\n");
- return EXIT_FAILURE;
- } else {
- infile = strdup(argv[1]);
- rnds = atoi(argv[2]);
- printf("Beginning benchmarks.\n");
- printf("---------------------------------------------------------------------\n");
- }
- for (iii = 3; iii < (unsigned int) argc; iii++) {
- nbench = 0;
- while (1) {
- thisbench = benchmarks[nbench++];
- if (!(thisbench.name && thisbench.fn)) {
- fprintf(stderr, "bad benchmark %s\n", argv[iii]);
- break;
- }
- if (strcmp(argv[iii], thisbench.name) == 0) {
- int rnd = 0;
- start = clock();
- for (rnd = 0; rnd<rnds; rnd++) {
- (*thisbench.fn)(rnd != rnds - 1);
- }
- end = clock();
- printf("Benchmark %s took %0.6fs per round [%d rounds]\n",
- thisbench.name,
- (float)(end - start) / (float)(CLOCKS_PER_SEC * rnds),
- rnds);
- printf("---------------------------------------------------------------------\n");
- break;
- }
- }
- }
- free(infile);
- return EXIT_SUCCESS;
-} /* ---------- end of function main ---------- */
diff --git a/src/libqes/test/data/bad_diff_lens.fastq b/src/libqes/test/data/bad_diff_lens.fastq
deleted file mode 100644
index c4dac0f..0000000
--- a/src/libqes/test/data/bad_diff_lens.fastq
+++ /dev/null
@@ -1,4 +0,0 @@
- at HWI-ST960:105:D10GVACXX:2:1101:1151:2158 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAANGACATTGAATCTATATGT
-+
-JJJJJIJHIJCC#4ADFFHHHGHJJJJIJJJ
diff --git a/src/libqes/test/data/bad_nohdr.fastq b/src/libqes/test/data/bad_nohdr.fastq
deleted file mode 100644
index 8a1eac8..0000000
--- a/src/libqes/test/data/bad_nohdr.fastq
+++ /dev/null
@@ -1,3 +0,0 @@
-CACGATCAGATCAANGACATTGAATCTATATGT
-+
-JJJJJJJIJHIJCC#4ADFFHHHGHJJJJIJJJ
diff --git a/src/libqes/test/data/bad_noqual.fastq b/src/libqes/test/data/bad_noqual.fastq
deleted file mode 100644
index 67d3a81..0000000
--- a/src/libqes/test/data/bad_noqual.fastq
+++ /dev/null
@@ -1,3 +0,0 @@
- at HWI-ST960:105:D10GVACXX:2:1101:1151:2158 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAANGACATTGAATCTATATGT
-+
diff --git a/src/libqes/test/data/bad_noqualhdrchr.fastq b/src/libqes/test/data/bad_noqualhdrchr.fastq
deleted file mode 100644
index 9f91fe1..0000000
--- a/src/libqes/test/data/bad_noqualhdrchr.fastq
+++ /dev/null
@@ -1,4 +0,0 @@
- at HWI-ST960:105:D10GVACXX:2:1101:1151:2158 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAANGACATTGAATCTATATGT
-
-CACGATCAGATCAANGACATTGAATCTATATGT
diff --git a/src/libqes/test/data/bad_noqualhdreol.fastq b/src/libqes/test/data/bad_noqualhdreol.fastq
deleted file mode 100644
index 5aaf3cc..0000000
--- a/src/libqes/test/data/bad_noqualhdreol.fastq
+++ /dev/null
@@ -1,3 +0,0 @@
- at HWI-ST960:105:D10GVACXX:2:1101:1151:2158 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAANGACATTGAATCTATATGT
-+HWI-BLERG
\ No newline at end of file
diff --git a/src/libqes/test/data/empty.fastq b/src/libqes/test/data/empty.fastq
deleted file mode 100644
index b516b2c..0000000
--- a/src/libqes/test/data/empty.fastq
+++ /dev/null
@@ -1 +0,0 @@
-@
\ No newline at end of file
diff --git a/src/libqes/test/data/empty.txt b/src/libqes/test/data/empty.txt
deleted file mode 100644
index e69de29..0000000
diff --git a/src/libqes/test/data/loremipsum.txt b/src/libqes/test/data/loremipsum.txt
deleted file mode 100644
index eaf1478..0000000
--- a/src/libqes/test/data/loremipsum.txt
+++ /dev/null
@@ -1,11 +0,0 @@
-Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec ornare tortor et
-rhoncus iaculis. Sed suscipit, arcu nec elementum vestibulum, tortor tortor
-dictum dui, eu sodales magna orci eu libero. Cras commodo, ligula tempor auctor
-vulputate, eros urna gravida eros, eget congue leo quam quis mi. Curabitur
-luctus augue nibh, eget vehicula augue commodo eget. Donec condimentum molestie
-adipiscing. In non purus lacus. Nam nec mollis mauris. Donec rhoncus, diam sit
-amet rhoncus viverra, lectus risus tincidunt ipsum, in dignissim justo purus
-eget enim. Fusce congue nulla egestas est auctor faucibus. Integer feugiat
-molestie leo, a interdum neque pretium nec. Etiam sit amet nibh leo.
-
-End of lorem ipsum.
diff --git a/src/libqes/test/data/loremipsum.txt.gz b/src/libqes/test/data/loremipsum.txt.gz
deleted file mode 100644
index cb768d6..0000000
Binary files a/src/libqes/test/data/loremipsum.txt.gz and /dev/null differ
diff --git a/src/libqes/test/data/nocomment.fasta b/src/libqes/test/data/nocomment.fasta
deleted file mode 100644
index 732a2b7..0000000
--- a/src/libqes/test/data/nocomment.fasta
+++ /dev/null
@@ -1,5 +0,0 @@
->HWI-ST960:105:D10GVACXX:2:1101:1122:2186
-CACACTTGAA
-TCCAGTTTAA
-AGTTAACTCA
-TTG
diff --git a/src/libqes/test/data/random.bin b/src/libqes/test/data/random.bin
deleted file mode 100644
index 9f95426..0000000
Binary files a/src/libqes/test/data/random.bin and /dev/null differ
diff --git a/src/libqes/test/data/test.fasta b/src/libqes/test/data/test.fasta
deleted file mode 100644
index f814857..0000000
--- a/src/libqes/test/data/test.fasta
+++ /dev/null
@@ -1,4061 +0,0 @@
->HWI-ST960:105:D10GVACXX:2:1101:1122:2186 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCAGTTTAA
-AGTTAACTCA
-TTG
->HWI-ST960:105:D10GVACXX:2:1101:1229:2187 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTGAGTTT
-TTGGACTGTA
-CAT
->HWI-ST960:105:D10GVACXX:2:1101:1175:2195 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTAATTGT
-CACTGTTTCA
-CCC
->HWI-ST960:105:D10GVACXX:2:1101:1175:2224 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTGTGACT
-CTGTTCCTGT
-TGT
->HWI-ST960:105:D10GVACXX:2:1101:1204:2232 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATCACAGA
-GCAGCAGTAT
-TTC
->HWI-ST960:105:D10GVACXX:2:1101:1237:2239 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTACACAC
-GTATATGCAA
-TAC
->HWI-ST960:105:D10GVACXX:2:1101:1123:2239 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAATAATGT
-GGTATTAGTC
-TG
->HWI-ST960:105:D10GVACXX:2:1101:1155:2246 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAGCCACTG
-AACTAAAAAA
-AAA
->HWI-ST960:105:D10GVACXX:2:1101:1443:2173 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTACCAAAG
-TCTGAATGAT
-TAT
->HWI-ST960:105:D10GVACXX:2:1101:1360:2176 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCCGGCTCT
-GTCTCTCTCT
-CCC
->HWI-ST960:105:D10GVACXX:2:1101:1272:2183 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATCATTTA
-GAGGAAGGAG
-AA
->HWI-ST960:105:D10GVACXX:2:1101:1423:2185 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTATGACGT
-CAAATTATGC
-CT
->HWI-ST960:105:D10GVACXX:2:1101:1398:2186 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAAAAAAAA
-AAAGAATAAA
-GAA
->HWI-ST960:105:D10GVACXX:2:1101:1333:2199 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTATTACAA
-AGTTTACATC
-TCT
->HWI-ST960:105:D10GVACXX:2:1101:1388:2214 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTCGTCT
-TCCATTTCTA
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:1366:2229 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTATGTAT
-ATGCTGTGGT
-AG
->HWI-ST960:105:D10GVACXX:2:1101:1297:2232 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCATTCATGT
-TGATATATTT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:1374:2245 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTGTGTGT
-CTGAAGTAGT
-TGA
->HWI-ST960:105:D10GVACXX:2:1101:1277:2249 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATGTTTCA
-GACTTCGAGA
-AGC
->HWI-ST960:105:D10GVACXX:2:1101:1425:2250 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTATATAC
-TTCACAACTC
-TG
->HWI-ST960:105:D10GVACXX:2:1101:1601:2174 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGA
-TCTTTTACGT
-AGACGATGTG
-CC
->HWI-ST960:105:D10GVACXX:2:1101:1581:2174 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCAGTTGAG
-GAACTATTGT
-TTC
->HWI-ST960:105:D10GVACXX:2:1101:1717:2186 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCAATCTTTG
-TACTGTTGAA
-CAA
->HWI-ST960:105:D10GVACXX:2:1101:1538:2187 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAACTGTTT
-GTGTCAATCA
-TT
->HWI-ST960:105:D10GVACXX:2:1101:1687:2195 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTGTCCTTC
-GGATCACTCA
-A
->HWI-ST960:105:D10GVACXX:2:1101:1589:2195 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTGAGCACA
-AAGATGATCA
-AAC
->HWI-ST960:105:D10GVACXX:2:1101:1611:2205 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTGAGAGT
-AGCTCTGTTT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:1672:2207 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTATATTTG
-ATACATCGGT
-TC
->HWI-ST960:105:D10GVACXX:2:1101:1595:2220 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTCTGACT
-GATGAACATA
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:1706:2224 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTGTGCAAT
-TAGTGCAACT
-GA
->HWI-ST960:105:D10GVACXX:2:1101:1575:2228 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCGTTTGAGA
-CTCTATCTTA
-CCT
->HWI-ST960:105:D10GVACXX:2:1101:1557:2229 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATTTTTGT
-GTGTACTTGT
-CC
->HWI-ST960:105:D10GVACXX:2:1101:1747:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTATATACA
-ATTGTGGACT
-AC
->HWI-ST960:105:D10GVACXX:2:1101:1921:2172 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTTTTAGA
-ACTCTTTTCC
-TA
->HWI-ST960:105:D10GVACXX:2:1101:1992:2192 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTTGTTGG
-GGTAAAAAAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:1925:2197 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTAAGTGT
-GATTCTTTTG
-G
->HWI-ST960:105:D10GVACXX:2:1101:1792:2234 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTAAAGTC
-ATGTCTTTGT
-TGT
->HWI-ST960:105:D10GVACXX:2:1101:1771:2239 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGGTGACCG
-AGAAATGTTT
-AA
->HWI-ST960:105:D10GVACXX:2:1101:1915:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTCAGTCT
-AACTAAAGTA
-TT
->HWI-ST960:105:D10GVACXX:2:1101:1899:2246 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCACTAATA
-CAATTGTTGC
-TC
->HWI-ST960:105:D10GVACXX:2:1101:2049:2181 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTGTTCTTG
-TACTACAGTG
-AT
->HWI-ST960:105:D10GVACXX:2:1101:2035:2185 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATGTAGAA
-TTCAGAATGT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:2214:2203 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCTGTACACG
-GCTTAATTTA
-TT
->HWI-ST960:105:D10GVACXX:2:1101:2244:2217 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCGGTTTGA
-GTGTTGCAAA
-TCT
->HWI-ST960:105:D10GVACXX:2:1101:2185:2223 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCAACAAGGT
-CGTTGTAGTA
-TAG
->HWI-ST960:105:D10GVACXX:2:1101:2067:2226 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATTCCATA
-GATTGTAGCC
-TC
->HWI-ST960:105:D10GVACXX:2:1101:2032:2227 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTTTGTTA
-GTTACGCTTT
-GC
->HWI-ST960:105:D10GVACXX:2:1101:2011:2230 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTAATAT
-GATATGAAAA
-TCT
->HWI-ST960:105:D10GVACXX:2:1101:2444:2173 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTTCCTGT
-GATTTGCAAT
-TTC
->HWI-ST960:105:D10GVACXX:2:1101:2254:2194 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCCATAAAA
-AGTCTCTACA
-AT
->HWI-ST960:105:D10GVACXX:2:1101:2448:2203 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAGAAGAAA
-AAGATGACCA
-GCT
->HWI-ST960:105:D10GVACXX:2:1101:2342:2213 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAATGTTCG
-ACTGTGAACC
-TTC
->HWI-ST960:105:D10GVACXX:2:1101:2268:2215 1:N:0: bcd:RPI3 seq:CACTTAGGCATC
-CACTTAGGCA
-TCAATATCAG
-AACTCGTTAT
-ATT
->HWI-ST960:105:D10GVACXX:2:1101:2411:2223 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGA
-TCGCAACTGT
-AGCAAGAAGA
-AAC
->HWI-ST960:105:D10GVACXX:2:1101:2292:2229 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTTTACTT
-AAAGAGCCCT
-AAC
->HWI-ST960:105:D10GVACXX:2:1101:2448:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATGAGTGT
-AGGCTTACTT
-AC
->HWI-ST960:105:D10GVACXX:2:1101:2389:2235 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTCGATCT
-GGTTTGTAGA
-AC
->HWI-ST960:105:D10GVACXX:2:1101:2675:2178 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTAAGTGA
-ACTCTGTGCG
-TCT
->HWI-ST960:105:D10GVACXX:2:1101:2548:2190 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAATCTTCT
-GTTGACTCAT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:2610:2203 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTAGTAT
-CAATTGAACT
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:2657:2203 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCATATATA
-TATAAATGCA
-GAC
->HWI-ST960:105:D10GVACXX:2:1101:2576:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATATTTTT
-CCCACTGTGT
-TCT
->HWI-ST960:105:D10GVACXX:2:1101:2626:2215 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGAGAACTC
-TAGAAACCTG
-CTT
->HWI-ST960:105:D10GVACXX:2:1101:2660:2219 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTCTACAAT
-GTACTGGAAA
-CTT
->HWI-ST960:105:D10GVACXX:2:1101:2509:2223 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTCAAACTT
-TATGTAAACT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:2536:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCATACCAA
-ATAGAATTTC
-TG
->HWI-ST960:105:D10GVACXX:2:1101:2584:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTGTGCCT
-GGATTAATAT
-GA
->HWI-ST960:105:D10GVACXX:2:1101:2674:2235 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATGCAACT
-GCAAATTCTG
-CA
->HWI-ST960:105:D10GVACXX:2:1101:2718:2235 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCACGGAACC
-AGTGACCGTC
-GT
->HWI-ST960:105:D10GVACXX:2:1101:2630:2245 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTACTTGA
-ACAGGATCTG
-TT
->HWI-ST960:105:D10GVACXX:2:1101:2869:2185 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCTCCGATG
-ATGATCAAAT
-CAT
->HWI-ST960:105:D10GVACXX:2:1101:2917:2207 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAAGTCTCG
-CTTATGACTA
-TGA
->HWI-ST960:105:D10GVACXX:2:1101:2789:2236 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATATTGGT
-CTGTATTGTG
-CTC
->HWI-ST960:105:D10GVACXX:2:1101:2841:2242 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAAGAACTA
-ACAGATATAT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:3211:2194 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTATGTAAT
-GTAGTCTTTA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:3145:2195 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTGGCTGTG
-GAGTAAAAAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:3082:2195 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCACTGTGTT
-GGCGTTTTAT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:3160:2208 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCACTTGTTG
-GCCAAAAAAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:3135:2214 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCGACAGGAG
-AGGTGATCGG
-AGT
->HWI-ST960:105:D10GVACXX:2:1101:3213:2220 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTGTTCTGT
-TGAAGGAGCT
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:3036:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTATATAC
-TTCACAACTC
-TG
->HWI-ST960:105:D10GVACXX:2:1101:3140:2228 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAGCAAATA
-AGTCAAAACT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:3106:2228 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCTTAGCTCG
-ACCTAACACT
-T
->HWI-ST960:105:D10GVACXX:2:1101:3085:2237 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCTCATCAAC
-TTTGTCTCTG
-CTT
->HWI-ST960:105:D10GVACXX:2:1101:3151:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAATTCCAT
-GTACTTACAT
-TCC
->HWI-ST960:105:D10GVACXX:2:1101:3041:2247 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTGTAATAC
-CTTTTATATA
-TAG
->HWI-ST960:105:D10GVACXX:2:1101:3218:2248 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAGCCCAAA
-CTGCATGCAC
-AT
->HWI-ST960:105:D10GVACXX:2:1101:3440:2193 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTTGGATT
-GAAGGGAGCT
-C
->HWI-ST960:105:D10GVACXX:2:1101:3302:2194 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCAAGTCAT
-GACTCATGAG
-CTA
->HWI-ST960:105:D10GVACXX:2:1101:3369:2202 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATTGTCAT
-ATTTGCGATG
-TAT
->HWI-ST960:105:D10GVACXX:2:1101:3257:2202 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTATGTAAA
-CTCTCGTGTG
-GCT
->HWI-ST960:105:D10GVACXX:2:1101:3285:2210 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTGAGATGC
-AAAACAGTAG
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:3316:2236 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTAAATC
-TTAATCTCAA
-AT
->HWI-ST960:105:D10GVACXX:2:1101:3597:2170 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTCCCCCG
-TGAGTTACTT
-CAC
->HWI-ST960:105:D10GVACXX:2:1101:3651:2176 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTATATGTA
-GGCTAAAAAA
-AAA
->HWI-ST960:105:D10GVACXX:2:1101:3568:2179 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTATTTATG
-TTTTGGACTT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:3545:2181 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATGTGTGT
-TGTGGTTTTT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:3669:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCACTGTGTT
-GGCGTTTTAT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:3587:2184 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTAAGTGT
-AGAATGCATA
-CAA
->HWI-ST960:105:D10GVACXX:2:1101:3570:2218 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTGTTGTAT
-GATTGAAGAA
-AT
->HWI-ST960:105:D10GVACXX:2:1101:3530:2235 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTAACGAAA
-ACTATTTAAA
-AT
->HWI-ST960:105:D10GVACXX:2:1101:3706:2247 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAAGGCGAG
-TGTATCTCAA
-CAA
->HWI-ST960:105:D10GVACXX:2:1101:3775:2173 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTACATTA
-AGGCAGTTCA
-TTG
->HWI-ST960:105:D10GVACXX:2:1101:3902:2188 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTCACAAA
-TGAACTTAAA
-CT
->HWI-ST960:105:D10GVACXX:2:1101:3885:2192 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTACCTACT
-CGTCGTACAT
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:3807:2204 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCATCTCGG
-ACCAAAGAGA
-GC
->HWI-ST960:105:D10GVACXX:2:1101:3780:2206 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTGCATGTT
-GTGCACCGGC
-TCC
->HWI-ST960:105:D10GVACXX:2:1101:3853:2215 1:N:0: bcd:RPI3 seq:CACTTAGGCATC
-CACTTAGGCA
-TCTCCGATGA
-TGATCAAATC
-AT
->HWI-ST960:105:D10GVACXX:2:1101:3946:2218 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTAGTCT
-TTTGGTATTT
-TA
->HWI-ST960:105:D10GVACXX:2:1101:3976:2221 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATTGTTCG
-GCTTTGGATT
-AAG
->HWI-ST960:105:D10GVACXX:2:1101:3866:2227 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAATACGAT
-ATGTATATGT
-AC
->HWI-ST960:105:D10GVACXX:2:1101:3816:2234 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTAGGTCT
-TGTGTAGAAA
-CT
->HWI-ST960:105:D10GVACXX:2:1101:3779:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTTTGAGT
-TTCGAGTTAT
-CTG
->HWI-ST960:105:D10GVACXX:2:1101:3799:2247 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATTCTATC
-TACTACTTTT
-TC
->HWI-ST960:105:D10GVACXX:2:1101:3759:2247 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAACTAGTA
-TAGTCAGAAA
-AT
->HWI-ST960:105:D10GVACXX:2:1101:3912:2249 1:N:0: bcd:RPI3 seq:CACTTAGGCATC
-CACTTAGGCA
-TCATGTGAAC
-AAGAACATAT
-CCT
->HWI-ST960:105:D10GVACXX:2:1101:4099:2173 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCTTGGCTCA
-TGAAGTAAAA
-TAA
->HWI-ST960:105:D10GVACXX:2:1101:4193:2190 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCACTTTACA
-GCTTCTTCTT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:4045:2192 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCACTGTGTT
-GGCGTTTTAT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:4171:2195 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGA
-TCGAAGTTGA
-AGAACCTATA
-A
->HWI-ST960:105:D10GVACXX:2:1101:4159:2232 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCGTATCAAA
-CGTAGAGGCA
-G
->HWI-ST960:105:D10GVACXX:2:1101:4186:2233 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTTAGTCA
-GCTGCAACAC
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:4072:2235 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTAACACCA
-AACAACTCTT
-TCT
->HWI-ST960:105:D10GVACXX:2:1101:4053:2236 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTTGGAGG
-TTTGAGATAT
-AA
->HWI-ST960:105:D10GVACXX:2:1101:4001:2239 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTCAAATGA
-GAACTTTGAA
-GGC
->HWI-ST960:105:D10GVACXX:2:1101:4487:2169 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAAGCATGT
-AGTTTGATGA
-TC
->HWI-ST960:105:D10GVACXX:2:1101:4487:2182 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAAATTGTT
-ACGCAACAAA
-CT
->HWI-ST960:105:D10GVACXX:2:1101:4428:2194 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTAAATAT
-TTTTTCTATT
-CA
->HWI-ST960:105:D10GVACXX:2:1101:4264:2201 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCACTTAATC
-TGAGTCTCTG
-CTT
->HWI-ST960:105:D10GVACXX:2:1101:4422:2216 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCACTTTACA
-CGACAAAATA
-A
->HWI-ST960:105:D10GVACXX:2:1101:4332:2220 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTTCCGA
-GTACAACTTT
-GG
->HWI-ST960:105:D10GVACXX:2:1101:4424:2238 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTAATCTTG
-TGTCGGCAGG
-TGT
->HWI-ST960:105:D10GVACXX:2:1101:4369:2249 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCGATAATGA
-TGATGAAAGA
-TG
->HWI-ST960:105:D10GVACXX:2:1101:4279:2250 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTATGTAG
-AACTCTTTGC
-TT
->HWI-ST960:105:D10GVACXX:2:1101:4583:2173 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTAGTGA
-AATACACTCT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:4599:2173 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTGTTATC
-GTGTCTGTAA
-GC
->HWI-ST960:105:D10GVACXX:2:1101:4699:2181 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTGCCTTC
-AAGTTAACTT
-TGT
->HWI-ST960:105:D10GVACXX:2:1101:4615:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAGTCTTCT
-TCTTCTGTAT
-TA
->HWI-ST960:105:D10GVACXX:2:1101:4505:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATCCTATG
-CTTTGGTCAT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:4515:2195 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTACTTAG
-ACTCATGCTT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:4695:2199 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCAATGACTG
-TAACTTACTC
-TTC
->HWI-ST960:105:D10GVACXX:2:1101:4586:2200 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTATAGGA
-ATCTGTAACT
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:4624:2201 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTATTTGCG
-ATGTATCATG
-TAT
->HWI-ST960:105:D10GVACXX:2:1101:4717:2204 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTTTGGTT
-TATTTACATG
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:4738:2224 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATAGCTTC
-TCTGTTATGT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:4745:2243 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTGATAT
-CTAAGCTTAT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:4619:2246 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTCAGATT
-TCTTACATTC
-AA
->HWI-ST960:105:D10GVACXX:2:1101:4707:2246 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCAGTGTTT
-GTCTGAACTC
-TG
->HWI-ST960:105:D10GVACXX:2:1101:4754:2182 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATCGTCGT
-CAAGCCTGCC
-AC
->HWI-ST960:105:D10GVACXX:2:1101:4768:2182 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAAACTTCT
-CTGTTTAGTT
-TGT
->HWI-ST960:105:D10GVACXX:2:1101:4842:2184 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTAATCAT
-TATAGAGATG
-GT
->HWI-ST960:105:D10GVACXX:2:1101:4964:2184 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCAAGTCAT
-GACTCATGAG
-AT
->HWI-ST960:105:D10GVACXX:2:1101:4787:2188 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAACAAACT
-TGCATGTCGG
-CAC
->HWI-ST960:105:D10GVACXX:2:1101:4867:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTCTTCTTT
-CCAATCTTAT
-CAC
->HWI-ST960:105:D10GVACXX:2:1101:4934:2200 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTTGTAG
-TAACTGAAAA
-CG
->HWI-ST960:105:D10GVACXX:2:1101:4988:2205 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCTTCTTTC
-TCGAGAAATC
-GG
->HWI-ST960:105:D10GVACXX:2:1101:4973:2209 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTGCTGTAA
-TTACAGATTG
-AA
->HWI-ST960:105:D10GVACXX:2:1101:4783:2210 1:N:0: bcd:RPI3 seq:CACTTAGGCATC
-CACTTAGGCA
-TCGATGAATA
-CATCATGGTA
-GTG
->HWI-ST960:105:D10GVACXX:2:1101:4861:2212 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTATGTTT
-AGTTTAGAAG
-AA
->HWI-ST960:105:D10GVACXX:2:1101:4929:2223 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAACTGTGT
-CTCATCACTC
-AA
->HWI-ST960:105:D10GVACXX:2:1101:4966:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATATTCAA
-ACTCTTGGAC
-TGA
->HWI-ST960:105:D10GVACXX:2:1101:4877:2249 1:N:0: bcd:RPI2 seq:CACCGATGTATC
-CACCGATGTA
-TCCTTCCTAC
-TTGAAGAAGG
-TTG
->HWI-ST960:105:D10GVACXX:2:1101:5029:2168 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGA
-TCTTTTGGTT
-CTGTAGACAC
-AC
->HWI-ST960:105:D10GVACXX:2:1101:5174:2170 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTATATAAT
-ATTCCCTAAG
-AA
->HWI-ST960:105:D10GVACXX:2:1101:5153:2178 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAATACCCC
-GAAAATTAGA
-TC
->HWI-ST960:105:D10GVACXX:2:1101:5078:2188 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTCTTGGTC
-TGGTGGTAAC
-AAT
->HWI-ST960:105:D10GVACXX:2:1101:5182:2192 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATTTGTCA
-ACTTCAATTT
-CAG
->HWI-ST960:105:D10GVACXX:2:1101:5054:2198 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTACTGTA
-TCTCATTAGC
-TGA
->HWI-ST960:105:D10GVACXX:2:1101:5208:2202 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTATGTTTC
-TCTTGGAACG
-AA
->HWI-ST960:105:D10GVACXX:2:1101:5105:2206 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCATGAACTG
-TATTAAACTT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:5029:2212 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAACATTTC
-GAACAATGAA
-CAA
->HWI-ST960:105:D10GVACXX:2:1101:5084:2222 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTACCTCT
-CTCTGACTTC
-AC
->HWI-ST960:105:D10GVACXX:2:1101:5223:2223 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCCGGAGTTT
-TTTCAGCAGT
-TC
->HWI-ST960:105:D10GVACXX:2:1101:5173:2228 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTATGTGT
-AATGATTCCT
-TC
->HWI-ST960:105:D10GVACXX:2:1101:5208:2240 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATTTACTT
-TGATCAGAAA
-TT
->HWI-ST960:105:D10GVACXX:2:1101:5101:2247 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAAACTCTA
-CCTTTATTAC
-AGT
->HWI-ST960:105:D10GVACXX:2:1101:5189:2247 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCTACAAAA
-CTTTCTAATT
-TG
->HWI-ST960:105:D10GVACXX:2:1101:5018:2248 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTATGTAG
-AATATGAGTT
-TA
->HWI-ST960:105:D10GVACXX:2:1101:5160:2249 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTGCTTGA
-TTTTGAAGTT
-AG
->HWI-ST960:105:D10GVACXX:2:1101:5498:2182 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAGCGAGAG
-TTCTTGAACT
-GA
->HWI-ST960:105:D10GVACXX:2:1101:5435:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTATAAGGA
-CTGTGAAGTG
-TG
->HWI-ST960:105:D10GVACXX:2:1101:5472:2190 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCACTGTAA
-TCTCACGGTG
-TGT
->HWI-ST960:105:D10GVACXX:2:1101:5358:2205 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTATGTAAT
-GTAGTCTTTA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:5420:2213 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCGTTTGAT
-TTGCAAGCTG
->HWI-ST960:105:D10GVACXX:2:1101:5318:2214 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATTTGTAG
-CAAGGCACTG
-AT
->HWI-ST960:105:D10GVACXX:2:1101:5357:2223 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCTTCATTT
-CTGCTCTTAT
-CAC
->HWI-ST960:105:D10GVACXX:2:1101:5300:2224 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAATGTAGA
-ACACACATGA
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:5485:2228 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAAAATATC
-GTATCCGTTC
-AA
->HWI-ST960:105:D10GVACXX:2:1101:5295:2241 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCAAAGACT
-TGGACCTTCT
-TTC
->HWI-ST960:105:D10GVACXX:2:1101:5281:2244 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGGAGCGTA
-CCGACATGCG
-GT
->HWI-ST960:105:D10GVACXX:2:1101:5679:2172 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTAACAATA
-TTCTCATGCA
-CCT
->HWI-ST960:105:D10GVACXX:2:1101:5663:2184 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTTTGTAA
-TCTGACTCTC
-TT
->HWI-ST960:105:D10GVACXX:2:1101:5539:2195 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTGAAAGA
-AAGAGCCATT
-GGT
->HWI-ST960:105:D10GVACXX:2:1101:5728:2197 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATCTGTAT
-AAATAGTTTT
-AA
->HWI-ST960:105:D10GVACXX:2:1101:5500:2203 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTATCAAT
-TGAACTAGAT
-TCA
->HWI-ST960:105:D10GVACXX:2:1101:5592:2204 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGA
-TCAATAAAGC
-TGTTGAATGA
-GAT
->HWI-ST960:105:D10GVACXX:2:1101:5553:2233 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCGATCTGTA
-AACTAAAAAA
-AC
->HWI-ST960:105:D10GVACXX:2:1101:5604:2241 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATTTGATT
-ACCATAGCAT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:5743:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAAGGTTTT
-AAGTTCTTAG
-AAC
->HWI-ST960:105:D10GVACXX:2:1101:5682:2243 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTCTTGAGT
-ATGTAGAATC
-TG
->HWI-ST960:105:D10GVACXX:2:1101:5979:2179 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCTCTCTAG
-AAAATATCAG
-A
->HWI-ST960:105:D10GVACXX:2:1101:5958:2186 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTGCGATGA
-TGATAAAATA
-GC
->HWI-ST960:105:D10GVACXX:2:1101:5985:2215 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTATAGTT
-TTGTTGTTTC
-TT
->HWI-ST960:105:D10GVACXX:2:1101:5952:2229 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTAGCAGTA
-CAATTGCAGA
-AGT
->HWI-ST960:105:D10GVACXX:2:1101:5970:2231 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCTTATGTA
-GTCTCATTTC
-CT
->HWI-ST960:105:D10GVACXX:2:1101:5909:2233 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCACCAGTTT
-TACAGAGTGT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:5792:2239 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTATATAC
-TTCACAACTC
-TG
->HWI-ST960:105:D10GVACXX:2:1101:5990:2248 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCACGGGAAG
-GTGATATTTG
-CT
->HWI-ST960:105:D10GVACXX:2:1101:6014:2179 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTACTTCT
-AAGTTTAGTA
-AC
->HWI-ST960:105:D10GVACXX:2:1101:6138:2192 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCTTTATAT
-GAACCAATAA
-TAG
->HWI-ST960:105:D10GVACXX:2:1101:6181:2194 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATCACAAA
-ATATATAGGA
-AGT
->HWI-ST960:105:D10GVACXX:2:1101:6001:2199 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTTGTGAA
-TCTGATTATA
-CAC
->HWI-ST960:105:D10GVACXX:2:1101:6161:2202 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTAAGTCA
-TAATAATAGT
-AGC
->HWI-ST960:105:D10GVACXX:2:1101:6053:2206 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTTTGTTG
-GCATGAGAAC
-CAA
->HWI-ST960:105:D10GVACXX:2:1101:6128:2212 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCATTGTTG
-TACTCTTTAA
-TAT
->HWI-ST960:105:D10GVACXX:2:1101:6082:2221 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATTTTGTG
-TGAAAAAAAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:6229:2231 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTTTGGTG
-AAGTTTTTAA
-GT
->HWI-ST960:105:D10GVACXX:2:1101:6024:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTAAACCT
-ATAATATTTC
-TT
->HWI-ST960:105:D10GVACXX:2:1101:6181:2236 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTCGGCTAA
-TACCTAATGT
-CA
->HWI-ST960:105:D10GVACXX:2:1101:6060:2238 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTGAATCA
-TGTTGCTTTA
-CT
->HWI-ST960:105:D10GVACXX:2:1101:6084:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAATGTGTT
-CTCTCTGTTC
-AA
->HWI-ST960:105:D10GVACXX:2:1101:6492:2184 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCTTCACAT
-TATGAATATC
-AA
->HWI-ST960:105:D10GVACXX:2:1101:6252:2185 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTATATAC
-TTCACAACTC
-TG
->HWI-ST960:105:D10GVACXX:2:1101:6273:2186 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAATGTTGT
-CTCTCCCTCT
-TAT
->HWI-ST960:105:D10GVACXX:2:1101:6457:2201 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTGTGAAAC
-TCTATCAATT
-CA
->HWI-ST960:105:D10GVACXX:2:1101:6377:2203 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGAATATGT
-TGCTGTAGTC
-AC
->HWI-ST960:105:D10GVACXX:2:1101:6427:2203 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCAAACCAGA
-GACAAATGAC
-AC
->HWI-ST960:105:D10GVACXX:2:1101:6279:2218 1:N:0: bcd:RPI2 seq:CACCGATGTATC
-CACCGATGTA
-TCTTGGACTG
-TGAAGTTTGG
-CT
->HWI-ST960:105:D10GVACXX:2:1101:6366:2222 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAGATGTCG
-GCGTTGAATA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:6393:2231 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTATTGCAG
-TAGAACATAA
-GT
->HWI-ST960:105:D10GVACXX:2:1101:6268:2234 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAACTCTTG
-TGTACCATAA
-AAA
->HWI-ST960:105:D10GVACXX:2:1101:6467:2241 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTATCACCA
-TGTTCCAATT
-TC
->HWI-ST960:105:D10GVACXX:2:1101:6481:2244 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAATACTAG
-TGTTTAAGAA
-GTT
->HWI-ST960:105:D10GVACXX:2:1101:6397:2246 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTAACTTT
-GGCGAATGGA
-TAC
->HWI-ST960:105:D10GVACXX:2:1101:6429:2247 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTATATAT
-GGAGAAAATG
-GA
->HWI-ST960:105:D10GVACXX:2:1101:6525:2176 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCACTGTAAG
-CTGAGGAACT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:6517:2192 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTATGGCAC
-GGCTATGAAA
-TCT
->HWI-ST960:105:D10GVACXX:2:1101:6700:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCACATCTCA
-CTGCTCACTA
-CTC
->HWI-ST960:105:D10GVACXX:2:1101:6538:2194 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTGCTAGAG
-AGAGGAGGAG
-AC
->HWI-ST960:105:D10GVACXX:2:1101:6575:2195 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTGTTTTAA
-CACCTCTACT
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:6501:2202 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCTTTATGG
-CTCTAGTACA
-AGC
->HWI-ST960:105:D10GVACXX:2:1101:6631:2202 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTATCTCT
-AAAATTGCAA
-AT
->HWI-ST960:105:D10GVACXX:2:1101:6672:2205 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGA
-TCATGGTTGC
-TTTAATATTT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:6579:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCGACTTTG
-ATCCAAAAAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:6552:2217 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCATCTTTAG
-CTTTATTTAC
-TC
->HWI-ST960:105:D10GVACXX:2:1101:6685:2223 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCATTATTA
-TCAATAGCTC
-TTC
->HWI-ST960:105:D10GVACXX:2:1101:6503:2223 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTTAGGGG
-CTGATTTGTC
-TT
->HWI-ST960:105:D10GVACXX:2:1101:6613:2224 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTCTACCAT
-TATGCACTAT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:6670:2231 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCGGCGTGA
-AAGGGCGACT
-AAA
->HWI-ST960:105:D10GVACXX:2:1101:6721:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTAAACTT
-TCTTAGCTTG
-TCC
->HWI-ST960:105:D10GVACXX:2:1101:6642:2234 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGGGTGATG
-AACGAAATAA
-AAA
->HWI-ST960:105:D10GVACXX:2:1101:6589:2242 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATTAAAGA
-CAGAGAGATA
-GA
->HWI-ST960:105:D10GVACXX:2:1101:6684:2245 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGATCGAAA
-CCAAACACCG
-AT
->HWI-ST960:105:D10GVACXX:2:1101:6830:2173 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCTTGTCAT
-TCTCTAAATA
-AC
->HWI-ST960:105:D10GVACXX:2:1101:6954:2174 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTATAACT
-CTCTCGCCTT
-TGT
->HWI-ST960:105:D10GVACXX:2:1101:6754:2179 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTAAGTCG
-TATCTAGGTG
-TGT
->HWI-ST960:105:D10GVACXX:2:1101:6877:2188 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAACAAAGT
-CGTTGTAGTA
-TAC
->HWI-ST960:105:D10GVACXX:2:1101:6970:2193 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATCACACT
-GTCAAATCCG
-AA
->HWI-ST960:105:D10GVACXX:2:1101:6918:2197 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATTCGGCT
-CTGTTCATAT
-AC
->HWI-ST960:105:D10GVACXX:2:1101:6851:2211 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTTTCTGG
-CTGTAGAATC
-TT
->HWI-ST960:105:D10GVACXX:2:1101:6836:2224 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCACGCACA
-CCGCGTGTAG
-AG
->HWI-ST960:105:D10GVACXX:2:1101:6948:2228 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCCGATAGAG
-AACCTTGCTG
-ACC
->HWI-ST960:105:D10GVACXX:2:1101:6923:2230 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTATTTTA
-TGTGGTGTTA
-CTT
->HWI-ST960:105:D10GVACXX:2:1101:6971:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATCAGTGA
-TGAAATTATG
-TC
->HWI-ST960:105:D10GVACXX:2:1101:6883:2236 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTGAGTGAG
-ATATAAAATG
-GG
->HWI-ST960:105:D10GVACXX:2:1101:6822:2246 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGAATTCAG
-ACTGTGAAAC
-TGC
->HWI-ST960:105:D10GVACXX:2:1101:7018:2176 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGA
-TCGGAGTTTT
-TTCAGCAGTT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:7182:2176 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATTGTATT
-TGTGCGTGTA
-GC
->HWI-ST960:105:D10GVACXX:2:1101:7145:2178 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATAATAAG
-ACTCTTAATC
-AA
->HWI-ST960:105:D10GVACXX:2:1101:7091:2178 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTATGTAAT
-GTAGTCTTAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:7123:2181 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTCCTTGA
-CTGGAAAAAT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:7068:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTAATGTA
-CCGATGCATA
-GT
->HWI-ST960:105:D10GVACXX:2:1101:7245:2192 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTGTTTACC
-ATGGAACGAA
-CAT
->HWI-ST960:105:D10GVACXX:2:1101:7109:2196 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATTGTAAT
-TCAGTTAGCT
-CAA
->HWI-ST960:105:D10GVACXX:2:1101:7209:2197 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTTGTCAA
-TGCATAGACA
-AAA
->HWI-ST960:105:D10GVACXX:2:1101:7060:2201 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTGTGTGT
-TGGTGGATAT
-AAC
->HWI-ST960:105:D10GVACXX:2:1101:7155:2215 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTTGTTGG
-CCTTTAAAAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:7198:2217 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTATATAT
-TTCGTTTCAT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:7115:2229 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTAAGGCT
-GTGGAGGTTA
-TC
->HWI-ST960:105:D10GVACXX:2:1101:7149:2234 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTTTGTTA
-GACTCTTCGA
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:7127:2244 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTATGTAGA
-TACTGATATT
-A
->HWI-ST960:105:D10GVACXX:2:1101:7018:2247 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCTTTATAT
-GAACCAATAA
-TAG
->HWI-ST960:105:D10GVACXX:2:1101:7382:2185 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTAGTAGAC
-TTGCAAAGAT
-CGT
->HWI-ST960:105:D10GVACXX:2:1101:7449:2187 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAATACCCC
-GAAAATTAGA
-TC
->HWI-ST960:105:D10GVACXX:2:1101:7359:2193 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAGGCTGAT
-TGTAGAATGG
-TT
->HWI-ST960:105:D10GVACXX:2:1101:7292:2202 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTCAA
-TCCATGGTTT
-TCTCAAAGTT
-TTC
->HWI-ST960:105:D10GVACXX:2:1101:7393:2205 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTATGTCT
-CTGTACTGTA
-AC
->HWI-ST960:105:D10GVACXX:2:1101:7359:2210 1:N:0: bcd:RPI1 seq:CACATCACGATC
-CACATCACGA
-TCAGAGATCG
-GAAGAGATGG
-CTT
->HWI-ST960:105:D10GVACXX:2:1101:7415:2224 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATTAATTA
-TTCGTATGAA
-CT
->HWI-ST960:105:D10GVACXX:2:1101:7403:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCGTCTTAC
-CATTTCTTTC
-AT
->HWI-ST960:105:D10GVACXX:2:1101:7373:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTATGTCTG
-TCTAGTCTAT
-TG
->HWI-ST960:105:D10GVACXX:2:1101:7324:2231 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAATCAAAT
-GTATTATATA
-TAT
->HWI-ST960:105:D10GVACXX:2:1101:7309:2246 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTGAGTTT
-TTACATGTTT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:7475:2247 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTTGACTG
-TATTGAGCAA
-CC
->HWI-ST960:105:D10GVACXX:2:1101:7649:2170 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCTGAGTAGA
-CAATTTAATC
-A
->HWI-ST960:105:D10GVACXX:2:1101:7708:2170 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAGTTTAAT
-AAAACAGAAC
-AA
->HWI-ST960:105:D10GVACXX:2:1101:7709:2191 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTCTCTCTC
-TTACCTTTCT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:7690:2197 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATTCGATT
-AGTACCGTTA
-GTG
->HWI-ST960:105:D10GVACXX:2:1101:7607:2203 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCCGGAATG
-GTGCCTTTGT
-TAC
->HWI-ST960:105:D10GVACXX:2:1101:7698:2214 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCTCTGGCT
-TTGCTCAGAT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:7518:2217 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCAATTCTTT
-TACCGGGTTG
-AG
->HWI-ST960:105:D10GVACXX:2:1101:7534:2218 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATAATGAA
-TGTTTCGGAC
-TTC
->HWI-ST960:105:D10GVACXX:2:1101:7679:2220 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATCGGTGA
-GTGGAACTTC
-TT
->HWI-ST960:105:D10GVACXX:2:1101:7747:2228 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCACGAGTC
-GAGGCTCTCA
-ATA
->HWI-ST960:105:D10GVACXX:2:1101:7610:2232 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTCAGTGGT
-AGAGCGCGTG
-GC
->HWI-ST960:105:D10GVACXX:2:1101:7532:2235 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTATGTTC
-ACTGTTCTCT
-GC
->HWI-ST960:105:D10GVACXX:2:1101:7676:2238 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGA
-TCCAGCCGTC
-GGATACTGAC
-TT
->HWI-ST960:105:D10GVACXX:2:1101:7641:2240 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATCTGTAG
-CCTCTCTTTT
-AGT
->HWI-ST960:105:D10GVACXX:2:1101:7966:2176 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATGCAACT
-GCAAATTCTG
-CA
->HWI-ST960:105:D10GVACXX:2:1101:7948:2186 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTTGCTGT
-GGATGATCTG
-GT
->HWI-ST960:105:D10GVACXX:2:1101:7864:2190 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCGGAAGAAC
-TCTGGAAGTG
-AA
->HWI-ST960:105:D10GVACXX:2:1101:7912:2193 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAACAAGAT
-GTTTAATCAT
-CC
->HWI-ST960:105:D10GVACXX:2:1101:7970:2195 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCACAATTGT
-TGTCTTGTAG
-TA
->HWI-ST960:105:D10GVACXX:2:1101:7819:2202 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTAATTGT
-TTCTTAGCAT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:7762:2204 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTACTTTAT
-AAGGACTGTG
-AA
->HWI-ST960:105:D10GVACXX:2:1101:7847:2207 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATGCAACC
-CTGTCTTGCT
-TTA
->HWI-ST960:105:D10GVACXX:2:1101:7775:2219 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTATTGTG
-TTACTGAATC
-TT
->HWI-ST960:105:D10GVACXX:2:1101:7900:2219 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATTACGCC
-CGAACGCAAA
-CC
->HWI-ST960:105:D10GVACXX:2:1101:7800:2227 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCTCTTATGA
-TGTCAAAACT
-TTC
->HWI-ST960:105:D10GVACXX:2:1101:7973:2227 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTATGTGT
-TCTGCAGATC
-GA
->HWI-ST960:105:D10GVACXX:2:1101:7844:2229 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTTCGTTG
-GGTTTTCTTC
-AT
->HWI-ST960:105:D10GVACXX:2:1101:7863:2232 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATAAATTT
-TCGAAGGAGA
-CAA
->HWI-ST960:105:D10GVACXX:2:1101:7912:2234 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCGTGTGTAA
-CCTCATATGG
-AC
->HWI-ST960:105:D10GVACXX:2:1101:7940:2245 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCGTGTCAA
-GTGTAGAATC
-AA
->HWI-ST960:105:D10GVACXX:2:1101:8023:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATGTATCT
-TGTTGTTTAT
-CTA
->HWI-ST960:105:D10GVACXX:2:1101:8157:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTCAGTGGT
-AGAGCGCGTG
-GC
->HWI-ST960:105:D10GVACXX:2:1101:8117:2186 1:N:0: bcd:RPI3 seq:CACTTAGGCATC
-CACTTAGGCA
-TCACTGAATC
-GACTTTGGGC
-AAA
->HWI-ST960:105:D10GVACXX:2:1101:8197:2187 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATGGTGCT
-TAAAAAAAAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:8236:2188 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTATGTCG
-GCTTAAACTC
-TAT
->HWI-ST960:105:D10GVACXX:2:1101:8088:2193 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTATGGAAA
-TGTGCTATGG
-AC
->HWI-ST960:105:D10GVACXX:2:1101:8085:2226 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTCGCAGTC
-GCTAAGCGTC
-AC
->HWI-ST960:105:D10GVACXX:2:1101:8003:2228 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATATTTGT
-GGATGATGAA
-GA
->HWI-ST960:105:D10GVACXX:2:1101:8138:2242 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTATATGA
-TTCTACTTAG
-TCA
->HWI-ST960:105:D10GVACXX:2:1101:8069:2250 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTGGTACTA
-TGAACATTGT
-GAC
->HWI-ST960:105:D10GVACXX:2:1101:8355:2173 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTATGTGT
-AACCCTGTCC
-TT
->HWI-ST960:105:D10GVACXX:2:1101:8375:2177 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TATTGCTATA
-GAGTCACGCA
-TCT
->HWI-ST960:105:D10GVACXX:2:1101:8257:2177 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCACCTGGAG
-ACTCATGTGT
-TGA
->HWI-ST960:105:D10GVACXX:2:1101:8438:2178 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTTGGTTT
-GGATTTTGGT
-TA
->HWI-ST960:105:D10GVACXX:2:1101:8299:2178 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATCTCTGG
-CTGTTGAATA
-GA
->HWI-ST960:105:D10GVACXX:2:1101:8333:2183 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAGCTTGCA
-AGTTCTCTCT
-GAA
->HWI-ST960:105:D10GVACXX:2:1101:8309:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCACTGTGTT
-GGCGTTTTAT
-CTG
->HWI-ST960:105:D10GVACXX:2:1101:8363:2198 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCAAGCATG
-ATGAATTGAT
-GAG
->HWI-ST960:105:D10GVACXX:2:1101:8494:2200 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTTTGCAT
-TGATTGTGGT
-TAC
->HWI-ST960:105:D10GVACXX:2:1101:8291:2212 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGA
-TCTCTACTCT
-ACTAAACCTC
-TGT
->HWI-ST960:105:D10GVACXX:2:1101:8482:2215 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATCTTCCG
-TCTGTTTCTG
-AT
->HWI-ST960:105:D10GVACXX:2:1101:8322:2218 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCTTGACCGA
-TGCTCGGACA
-A
->HWI-ST960:105:D10GVACXX:2:1101:8388:2225 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGA
-TCGTGTGTAT
-TTAGTAATTC
-AT
->HWI-ST960:105:D10GVACXX:2:1101:8442:2226 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATTTTCTA
-TGTTGTTTGG
-TAG
->HWI-ST960:105:D10GVACXX:2:1101:8339:2233 1:N:0: bcd:RPI2 seq:CACCGATGTATC
-CACCGATGTA
-TCATCTCTAG
-AACTCTTTAT
-AAT
->HWI-ST960:105:D10GVACXX:2:1101:8376:2238 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATGTGTCA
-GATTCTAAAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:8457:2246 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCACTCTGTG
-GATTATGCTT
-TA
->HWI-ST960:105:D10GVACXX:2:1101:8627:2171 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAGGTAAAT
-TTGTCTGAAT
-TA
->HWI-ST960:105:D10GVACXX:2:1101:8743:2178 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATCATCTT
-TTCTTATGTA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:8722:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTATGTAG
-AGAAAGTGAT
-TA
->HWI-ST960:105:D10GVACXX:2:1101:8678:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTGATGTAT
-ATTTACGAGA
-TGT
->HWI-ST960:105:D10GVACXX:2:1101:8565:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTGTCCTTC
-GGATCACTCA
-ATT
->HWI-ST960:105:D10GVACXX:2:1101:8583:2192 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTAACGCT
-TTTATGTGCT
-TCT
->HWI-ST960:105:D10GVACXX:2:1101:8633:2194 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTATACATA
-TTGGGTTGTG
-ATT
->HWI-ST960:105:D10GVACXX:2:1101:8687:2198 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATTTCTGT
-AGACTATGTG
-TTG
->HWI-ST960:105:D10GVACXX:2:1101:8605:2201 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGA
-TCTTTCTTGT
-CTAGTCGGTT
-TAT
->HWI-ST960:105:D10GVACXX:2:1101:8532:2207 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAATGAATG
-TGTAGAAAAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:8688:2216 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTGGGGAA
-GGATCAGATG
-CA
->HWI-ST960:105:D10GVACXX:2:1101:8560:2228 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAATTGGTG
-CCTGTAGGTC
-AG
->HWI-ST960:105:D10GVACXX:2:1101:8658:2230 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCTGCTATA
-GAATCTGGAC
-AAA
->HWI-ST960:105:D10GVACXX:2:1101:8538:2232 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTCTTATCT
-TTTACTTTCC
-TC
->HWI-ST960:105:D10GVACXX:2:1101:8669:2248 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTACTGTT
-TTTTCCGCCT
-TC
->HWI-ST960:105:D10GVACXX:2:1101:8917:2174 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATGTTGTT
-GTTGCATGCT
-GTG
->HWI-ST960:105:D10GVACXX:2:1101:8755:2195 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATGATGTC
-GTTGGGTCTT
-TGT
->HWI-ST960:105:D10GVACXX:2:1101:8885:2196 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCTCCGATGA
-TGATCAAATC
-AT
->HWI-ST960:105:D10GVACXX:2:1101:8967:2201 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTTCTTT
-ATTCCTGGGT
-TGT
->HWI-ST960:105:D10GVACXX:2:1101:8797:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTTAACTC
-TTGCCTCTTC
-TT
->HWI-ST960:105:D10GVACXX:2:1101:8831:2214 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTTTGGGT
-TTGTGGTGGG
-GGT
->HWI-ST960:105:D10GVACXX:2:1101:8957:2220 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTGTCTTTA
-GCATCGACTG
-TT
->HWI-ST960:105:D10GVACXX:2:1101:8751:2221 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTGTGTTTG
-TGTTTAAGTG
-CT
->HWI-ST960:105:D10GVACXX:2:1101:8914:2223 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCGTTTTGG
-CTTTCGTTCT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:8937:2229 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGA
-TCTGGAATGA
-TGATAACGAT
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:8832:2238 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTTGTCAG
-TCTAAGAAAA
-TG
->HWI-ST960:105:D10GVACXX:2:1101:8894:2244 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCGAATGTTT
-AAATTGGATC
-AA
->HWI-ST960:105:D10GVACXX:2:1101:8849:2246 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTTACTGT
-AGTATATATG
-AT
->HWI-ST960:105:D10GVACXX:2:1101:9130:2168 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAGGAATTG
-TTGAGTTTGG
-TA
->HWI-ST960:105:D10GVACXX:2:1101:9203:2174 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCTTGACTGT
-GATTTAAACG
-AG
->HWI-ST960:105:D10GVACXX:2:1101:9183:2182 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTACTCTA
-TCTTAAACAT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:9125:2192 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTATCGGAT
-TGTCAAATGT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:9001:2202 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCTTCTTGT
-TGTCTAACTC
-TC
->HWI-ST960:105:D10GVACXX:2:1101:9175:2204 1:N:0: bcd:RPI1 seq:CACATCACGATC
-CACATCACGA
-TCTGAGAATA
-AGAACATACA
-TAA
->HWI-ST960:105:D10GVACXX:2:1101:9224:2207 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATCGTAAA
-AACTTTGGGA
-TGC
->HWI-ST960:105:D10GVACXX:2:1101:9118:2208 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTATAGTTC
-AGTCGACATG
-AAT
->HWI-ST960:105:D10GVACXX:2:1101:9087:2209 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATATGGAT
-GGATAATTTT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:9013:2211 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAGGAGCCT
-CTGTAATTTT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:9153:2219 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCTCTTCGA
-ATGACGAGTT
-CC
->HWI-ST960:105:D10GVACXX:2:1101:9188:2234 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCCTTTGTCG
-CTAAGATTCG
-A
->HWI-ST960:105:D10GVACXX:2:1101:9022:2234 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTAAAATA
-AACACATGTA
-CTT
->HWI-ST960:105:D10GVACXX:2:1101:9098:2234 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCGAGGAGAG
-CAGTCTATTC
-TG
->HWI-ST960:105:D10GVACXX:2:1101:9115:2236 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTGTTTAG
-TTGGCGGTTT
-CAC
->HWI-ST960:105:D10GVACXX:2:1101:9136:2239 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTTTGCTT
-CCTTTAACAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:9477:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATTTATGG
-CACAACATGT
-AA
->HWI-ST960:105:D10GVACXX:2:1101:9421:2187 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCCCAGCCT
-CATAGAGGAA
-CTG
->HWI-ST960:105:D10GVACXX:2:1101:9299:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCACCAAACT
-TTTCAAACCA
-TGT
->HWI-ST960:105:D10GVACXX:2:1101:9456:2199 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAATTTCGG
-AAATGCTAAT
-CG
->HWI-ST960:105:D10GVACXX:2:1101:9347:2201 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGCATAATA
-ATGTATTTAT
-TTG
->HWI-ST960:105:D10GVACXX:2:1101:9436:2206 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTTATGAG
-TGTGCGTCTC
-AC
->HWI-ST960:105:D10GVACXX:2:1101:9384:2226 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTCTGTTA
-CACGCCGAGA
-TC
->HWI-ST960:105:D10GVACXX:2:1101:9328:2231 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCACTGTTGC
-AGTCGGTGTT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:9477:2238 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTATGTGT
-GCTGCTTTCT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:9563:2176 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCCTCGACA
-CTGTTACTCC
-AC
->HWI-ST960:105:D10GVACXX:2:1101:9614:2178 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATTGTCAT
-ATTTGCGATG
-TAT
->HWI-ST960:105:D10GVACXX:2:1101:9676:2191 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTTTAAAT
-CATTGTCTGA
-ATT
->HWI-ST960:105:D10GVACXX:2:1101:9526:2191 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAATCTTTT
-GTATTTTGCT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:9622:2195 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCTGTACCT
-GTTATGCTTT
-AAA
->HWI-ST960:105:D10GVACXX:2:1101:9597:2203 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAGTAGCTG
-TGGAATGAAA
-GT
->HWI-ST960:105:D10GVACXX:2:1101:9507:2209 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTCTAGAG
-CTCTGATGAG
-TT
->HWI-ST960:105:D10GVACXX:2:1101:9613:2210 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCTTTTCAT
-AACTCATCCT
-ACT
->HWI-ST960:105:D10GVACXX:2:1101:9741:2245 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTATGAGAC
-TGTATCCTTT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:9572:2247 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTATTAAA
-ATTAGAACAA
-AT
->HWI-ST960:105:D10GVACXX:2:1101:9606:2249 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTACATATA
-GTAGTGGAGG
-CCT
->HWI-ST960:105:D10GVACXX:2:1101:9995:2170 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTATGGGAA
-CTCTTTTGGA
-CC
->HWI-ST960:105:D10GVACXX:2:1101:9998:2188 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATCTTATT
-AGTTTTAACT
-TC
->HWI-ST960:105:D10GVACXX:2:1101:9771:2192 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCCCTATAAA
-TAAAAAACAG
-AC
->HWI-ST960:105:D10GVACXX:2:1101:9841:2194 1:N:0: bcd:RPI1 seq:CACATCACGATC
-CACATCACGA
-TCTACACCAA
-ACTCTGGTAC
-AGT
->HWI-ST960:105:D10GVACXX:2:1101:9751:2194 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAATTGTTG
-TAGGCTGTGG
-TCC
->HWI-ST960:105:D10GVACXX:2:1101:9885:2199 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTATGTTTG
-TGTAACTGTA
-AC
->HWI-ST960:105:D10GVACXX:2:1101:9758:2211 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTTGGCGA
-CTTTCTACCG
-CAC
->HWI-ST960:105:D10GVACXX:2:1101:9838:2213 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTGTAGCT
-CCATGAACAA
-AT
->HWI-ST960:105:D10GVACXX:2:1101:9815:2214 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTAATAAA
-CACAAAAGTT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:9945:2214 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCAGGATTG
-GTTTGGTGGA
-TTA
->HWI-ST960:105:D10GVACXX:2:1101:9878:2215 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTGAAGCC
-AGATCAGAAT
-CTT
->HWI-ST960:105:D10GVACXX:2:1101:9912:2218 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCAAAGTTA
-ATTTCTGTTT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:9753:2227 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTTACCAA
-ATAAGCTTAA
-GTC
->HWI-ST960:105:D10GVACXX:2:1101:9999:2231 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCTTTGTGAT
-ATCTGAAAAA
-CAT
->HWI-ST960:105:D10GVACXX:2:1101:9840:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTGATTTT
-TCCTTTGTTA
-TC
->HWI-ST960:105:D10GVACXX:2:1101:9928:2239 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTGCAAAGG
-CAAGGCTCTG
-CTG
->HWI-ST960:105:D10GVACXX:2:1101:9937:2249 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAGTCGGCT
-TAACTAAGGT
-GGA
->HWI-ST960:105:D10GVACXX:2:1101:9908:2249 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAAGAACTC
-TGTAATTTCT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:10129:2182 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTTGTCCT
-TAATTCATTT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:10012:2196 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTTTGTAT
-CCTTTCTCAT
-TTA
->HWI-ST960:105:D10GVACXX:2:1101:10236:2203 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATATCACC
-ATGTTCCAAT
-TTC
->HWI-ST960:105:D10GVACXX:2:1101:10124:2225 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAGTGTTGG
-CATGGGCCTC
-GA
->HWI-ST960:105:D10GVACXX:2:1101:10018:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTCGGTTGA
-CTGGAATTAT
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:10188:2243 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTTGTGAT
-TGTTGGCAAT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:10113:2246 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTAAGTGT
-AGAATGCATA
-C
->HWI-ST960:105:D10GVACXX:2:1101:10363:2184 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTGGATTCT
-TCGTTCAGGC
-CAT
->HWI-ST960:105:D10GVACXX:2:1101:10329:2196 1:N:0: bcd:RPI3 seq:CACTTAGGCATC
-CACTTAGGCA
-TCAAGACTGC
-AACAACTTCT
-GC
->HWI-ST960:105:D10GVACXX:2:1101:10309:2198 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTCTTCTGT
-CATCTACATA
-TGC
->HWI-ST960:105:D10GVACXX:2:1101:10373:2200 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAGTACTGT
-ATTTGCTATT
-CCC
->HWI-ST960:105:D10GVACXX:2:1101:10440:2212 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCTTTTCTT
-TTTGTCGGCA
-TC
->HWI-ST960:105:D10GVACXX:2:1101:10352:2213 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTATTATCT
-CTGTTGATTG
-AT
->HWI-ST960:105:D10GVACXX:2:1101:10470:2218 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCCTAGAAC
-TTGCTCAAAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:10322:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCACTGGAAC
-TCTTTCTTCT
-AA
->HWI-ST960:105:D10GVACXX:2:1101:10300:2236 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGAATCCAT
-AGTCTTACCA
-TGA
->HWI-ST960:105:D10GVACXX:2:1101:10348:2237 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTATGACA
-AGTCGAATCT
-ATT
->HWI-ST960:105:D10GVACXX:2:1101:10434:2240 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTATGTCG
-TTTCTTTGAA
-CT
->HWI-ST960:105:D10GVACXX:2:1101:10326:2249 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAAGAGTTG
-ATTGTGCAAA
-CAA
->HWI-ST960:105:D10GVACXX:2:1101:10707:2172 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTATTTAA
-ATTCCTTCAA
-GT
->HWI-ST960:105:D10GVACXX:2:1101:10553:2176 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTATGTGTA
-GACTTAATTT
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:10597:2193 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTAATGTA
-CCGATGCATA
-GTC
->HWI-ST960:105:D10GVACXX:2:1101:10566:2195 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTAGTTTT
-TGGATTGTAA
-ATT
->HWI-ST960:105:D10GVACXX:2:1101:10694:2196 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTTGTAA
-TGTTAAATAA
-CTC
->HWI-ST960:105:D10GVACXX:2:1101:10746:2198 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTAACAGGG
-ACAGTCGGGG
-GGT
->HWI-ST960:105:D10GVACXX:2:1101:10522:2206 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTCTGTAC
-AGATATACTT
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:10609:2213 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATTTGGCT
-TTTCTCTGCT
->HWI-ST960:105:D10GVACXX:2:1101:10672:2216 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTTGGACT
-CGGATACGCT
-TCA
->HWI-ST960:105:D10GVACXX:2:1101:10584:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGATGTTGA
-GGCTCAAAAG
-TT
->HWI-ST960:105:D10GVACXX:2:1101:10743:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTCGATAG
-AACTACAAAG
-AAT
->HWI-ST960:105:D10GVACXX:2:1101:10653:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTGTCCTTC
-GGATCACTCA
-AT
->HWI-ST960:105:D10GVACXX:2:1101:10642:2240 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAGATTTTA
-AAGTGTTACA
-AG
->HWI-ST960:105:D10GVACXX:2:1101:10627:2242 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAACAAGTT
-GGTCTGGGTT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:10734:2245 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTAATCTG
-GGATGAACTC
-AC
->HWI-ST960:105:D10GVACXX:2:1101:10579:2247 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAATCTTTA
-GTAGAACAAA
-ATC
->HWI-ST960:105:D10GVACXX:2:1101:10596:2249 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGGTACTAA
-TGGCGAAAGA
-AC
->HWI-ST960:105:D10GVACXX:2:1101:10984:2173 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATTACGAT
-GTCTCTGTAC
-TC
->HWI-ST960:105:D10GVACXX:2:1101:10870:2185 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATGGGTTC
-GACGTTAAAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:10979:2195 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAACTGAAA
-TGAACCAAAA
-CC
->HWI-ST960:105:D10GVACXX:2:1101:10780:2199 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTTGGTGG
-AACTACATTA
-TC
->HWI-ST960:105:D10GVACXX:2:1101:10858:2207 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTGTTTGCG
-GATTATGCGT
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:10924:2209 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAACAAAGT
-CGTTGTAGTA
-TAG
->HWI-ST960:105:D10GVACXX:2:1101:10881:2211 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCATACTGT
-GTCTGCTTCT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:10798:2212 1:N:0: bcd:RPI2 seq:CACCGATGTATC
-CACCGATGTA
-TCAATGTAGG
-TTGTTTTTGG
-AC
->HWI-ST960:105:D10GVACXX:2:1101:10962:2219 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTATAGGA
-ATCTGTAACT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:10898:2220 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTAATTTC
-GGCTGTAGCA
-TGT
->HWI-ST960:105:D10GVACXX:2:1101:10771:2225 1:N:0: bcd:RPI1 seq:CACATCACGATC
-CACATCACGA
-TCGAGAATGA
-TGAACCAATT
-AG
->HWI-ST960:105:D10GVACXX:2:1101:10861:2226 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTTGTTA
-GACTCTTCGA
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:10883:2230 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAAATGTTC
-TCTTTCTGAT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:10793:2238 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAACTAATG
-GATGTATGAA
-TAT
->HWI-ST960:105:D10GVACXX:2:1101:10996:2241 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTTTGTGT
-TGTTGACTCT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:10908:2243 1:N:0: bcd:RPI2 seq:CACCGATGTATC
-CACCGATGTA
-TCTGGAATGA
-TGATAACGAT
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:10822:2244 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTGTGTGTC
-TCAGAAAAAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:11150:2169 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTTGTAG
-TAACTGAAAA
-CGG
->HWI-ST960:105:D10GVACXX:2:1101:11176:2178 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTCTGTTGA
-CCAAAAAAAA
-A
->HWI-ST960:105:D10GVACXX:2:1101:11080:2183 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTCCATAA
-GCTTTGATCA
-CT
->HWI-ST960:105:D10GVACXX:2:1101:11039:2186 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTAGTTAGT
-TGTTTTAAAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:11213:2190 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCAATAAGAA
-TAAGAATAAG
-A
->HWI-ST960:105:D10GVACXX:2:1101:11039:2203 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAGAGAAAA
-TGAGCATTAT
-TAT
->HWI-ST960:105:D10GVACXX:2:1101:11145:2212 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTATGTTGT
-CTCTTAATCG
-GC
->HWI-ST960:105:D10GVACXX:2:1101:11168:2217 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAATCAATG
-CTGGTGCTAA
-CTT
->HWI-ST960:105:D10GVACXX:2:1101:11088:2218 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAAGAACAA
-GAACACATTT
-AC
->HWI-ST960:105:D10GVACXX:2:1101:11184:2224 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCACATCCTT
-TCAAAACAAG
-TTC
->HWI-ST960:105:D10GVACXX:2:1101:11073:2233 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTAAGTCT
-GGAATAGCTT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:11102:2235 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATTTGTCG
-AACTTGTAAA
-AAA
->HWI-ST960:105:D10GVACXX:2:1101:11129:2239 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGGTTGGTT
-ATACACCAAA
-CTC
->HWI-ST960:105:D10GVACXX:2:1101:11163:2245 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTAATAT
-GTCTGGCTTG
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:11321:2204 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAAATCTGT
-TTGGTTGTGG
-AA
->HWI-ST960:105:D10GVACXX:2:1101:11427:2204 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCTTCTTGG
-TAAAGGTTGA
-GT
->HWI-ST960:105:D10GVACXX:2:1101:11305:2204 1:N:0: bcd:RPI2 seq:CACCGATGTATC
-CACCGATGTA
-TCTACTGACC
-CCGAGGCTTT
-CGC
->HWI-ST960:105:D10GVACXX:2:1101:11259:2205 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAATATGTT
-TCGTAGAACT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:11401:2214 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTGTAGAAA
-ATGAACTATA
-AAT
->HWI-ST960:105:D10GVACXX:2:1101:11352:2220 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATTGAATA
-GTCGGGGTTA
-CTT
->HWI-ST960:105:D10GVACXX:2:1101:11437:2220 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATTGCGTC
-GTATGAGTAA
-AAG
->HWI-ST960:105:D10GVACXX:2:1101:11258:2232 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAACCGAGT
-ACTTTTGGTA
-GC
->HWI-ST960:105:D10GVACXX:2:1101:11443:2243 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTATGTAGT
-GTAGTGGTAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:11272:2245 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAGTGCTTC
-AACGGCTCTG
-GT
->HWI-ST960:105:D10GVACXX:2:1101:11399:2247 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGA
-TCATATGAAC
-TACGTGTGGC
-TT
->HWI-ST960:105:D10GVACXX:2:1101:11611:2171 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAGGAGCTC
-AAGAACGGAA
-GAT
->HWI-ST960:105:D10GVACXX:2:1101:11736:2174 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGAATACTG
-TGGTTGTTTT
-AG
->HWI-ST960:105:D10GVACXX:2:1101:11736:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTGATACAA
-TTTCGGTTTC
-GT
->HWI-ST960:105:D10GVACXX:2:1101:11623:2201 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTGTTTTG
-GGGTTTTAAA
-CAT
->HWI-ST960:105:D10GVACXX:2:1101:11724:2214 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTTAGGAC
-AGTTCATGTT
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:11676:2225 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTGCATCAA
-GCTGTAACCG
-AAC
->HWI-ST960:105:D10GVACXX:2:1101:11707:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGGTATGAA
-CTATGAACAC
-AA
->HWI-ST960:105:D10GVACXX:2:1101:11640:2237 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTTGTTA
-GACTCTTCGA
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:11532:2244 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCACTAGTAA
-TAGAGCTTGG
-AA
->HWI-ST960:105:D10GVACXX:2:1101:11511:2247 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATTGGAGA
-TATTGGTTAA
-CT
->HWI-ST960:105:D10GVACXX:2:1101:11573:2247 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAACAATTC
-GGCTAGAAAT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:11773:2169 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCTTTCTTAC
-TTCGGCCTGT
-T
->HWI-ST960:105:D10GVACXX:2:1101:11943:2187 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAAGATCAT
-ATGGACGTAA
-CAT
->HWI-ST960:105:D10GVACXX:2:1101:11759:2191 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATTGAGCT
-CTTCTTTTCT
-TA
->HWI-ST960:105:D10GVACXX:2:1101:11857:2196 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTCTGTAG
-TAGGCTTGCA
-TGC
->HWI-ST960:105:D10GVACXX:2:1101:11838:2200 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTATCAATG
-TATTGTATCC
-G
->HWI-ST960:105:D10GVACXX:2:1101:11790:2208 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTGAATTTC
-TGTAGACTAT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:11770:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGGATGCGA
-TCATACCAGC
-AC
->HWI-ST960:105:D10GVACXX:2:1101:11869:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCTGATGTT
-GGTTTGTAAT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:11959:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTACTGTA
-CACACAAACT
-TC
->HWI-ST960:105:D10GVACXX:2:1101:11892:2215 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAATAAAAT
-GACTCTGAAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:11899:2234 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTATAATGT
-AATAGTACTC
-ACC
->HWI-ST960:105:D10GVACXX:2:1101:12088:2170 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCTTTTGTA
-CAAATCCAAA
-CCT
->HWI-ST960:105:D10GVACXX:2:1101:12143:2181 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCTTCTGTC
-AACCTCTTCG
-GA
->HWI-ST960:105:D10GVACXX:2:1101:12198:2193 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCAGGGATGA
-TGATTCAATT
-A
->HWI-ST960:105:D10GVACXX:2:1101:12019:2199 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCATTGTTG
-AACTTAGAAT
-CAA
->HWI-ST960:105:D10GVACXX:2:1101:12174:2199 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTCTGTAG
-CTCTAGACCA
-TTC
->HWI-ST960:105:D10GVACXX:2:1101:12126:2204 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTATTCCCG
-TTGAGAGGAT
-CAT
->HWI-ST960:105:D10GVACXX:2:1101:12157:2207 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTGCTACTC
-TCCTCGTCTC
-CT
->HWI-ST960:105:D10GVACXX:2:1101:12048:2210 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTACCACTC
-TTGCATTTGC
-AT
->HWI-ST960:105:D10GVACXX:2:1101:12070:2217 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCACAGAGCT
-CTGATTAAAG
-TG
->HWI-ST960:105:D10GVACXX:2:1101:12006:2219 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTAGTTGA
-GCGGTTGAAT
-AC
->HWI-ST960:105:D10GVACXX:2:1101:12122:2230 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTCTGTAT
-GCTTTTTTGG
-GAC
->HWI-ST960:105:D10GVACXX:2:1101:12107:2231 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTCACAAC
-CTGTGAAAAT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:12066:2240 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTGTGGAT
-GATGAAGAGT
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:12166:2250 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCTGCAATA
-TTCTAAAGAA
-CTC
->HWI-ST960:105:D10GVACXX:2:1101:12124:2250 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGAATTTGG
-ATTTGATCAG
-TA
->HWI-ST960:105:D10GVACXX:2:1101:12436:2174 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTATAAAGT
-TAGTTGGTGG
-TTG
->HWI-ST960:105:D10GVACXX:2:1101:12303:2179 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATCTTTCT
-ACTTTCATTA
-AC
->HWI-ST960:105:D10GVACXX:2:1101:12490:2188 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCTTCAATT
-ATGAGTTTTC
-CA
->HWI-ST960:105:D10GVACXX:2:1101:12308:2196 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGA
-TCTATAGTTA
-AAAGAGCACT
-AA
->HWI-ST960:105:D10GVACXX:2:1101:12371:2201 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTGGTTTGG
-ACAAAAAAAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:12329:2218 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGA
-TCCTTTGTCG
-CTAAGATTCG
-A
->HWI-ST960:105:D10GVACXX:2:1101:12376:2223 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCTGATCAA
-GTACAAGGGT
-TAT
->HWI-ST960:105:D10GVACXX:2:1101:12362:2226 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTAATATC
-GCATTAGCCC
-AGT
->HWI-ST960:105:D10GVACXX:2:1101:12430:2229 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTAATATA
-CACTGAACTT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:12484:2235 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTAAGTTT
-CTATCAAAAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:12259:2237 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGCCTTGCT
-CTTCATTGGT
-TTC
->HWI-ST960:105:D10GVACXX:2:1101:12345:2240 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCCCGATAA
-ATAGAACGAT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:12290:2249 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTTGTCTG
-AAAAAAAAAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:12617:2173 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTAGTCT
-TATTGTATCT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:12673:2203 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTGATTCA
-AATCGATCCC
-T
->HWI-ST960:105:D10GVACXX:2:1101:12575:2204 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTTTATAT
-TATGTGAAGT
-AC
->HWI-ST960:105:D10GVACXX:2:1101:12730:2214 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTGAGTCG
-ATCGTAGAGT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:12674:2224 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTTTGTTT
-GATGTCTATG
-AT
->HWI-ST960:105:D10GVACXX:2:1101:12690:2226 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCACTAGCT
-TCTACTTTGA
-TAT
->HWI-ST960:105:D10GVACXX:2:1101:12653:2228 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATTGTTTC
-TGTCTATGAC
-TCC
->HWI-ST960:105:D10GVACXX:2:1101:12702:2234 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAGAGCCTT
-GTTTCTTATT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:12587:2240 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCTTATTGA
-TGATTCTATC
-TT
->HWI-ST960:105:D10GVACXX:2:1101:12614:2244 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTCGACATT
-TGGTGTGAAA
-TGC
->HWI-ST960:105:D10GVACXX:2:1101:12849:2171 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGCCCGACC
-TCGGACTGGG
-AAC
->HWI-ST960:105:D10GVACXX:2:1101:12894:2184 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAAAGTAGT
-CTCATCTTAT
-CAC
->HWI-ST960:105:D10GVACXX:2:1101:12816:2185 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTTAAAGG
-CTTATTATCA
-AAA
->HWI-ST960:105:D10GVACXX:2:1101:12946:2186 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTCTGATGA
-AATCTCATAT
-TGA
->HWI-ST960:105:D10GVACXX:2:1101:12964:2189 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCTAATATAT
-GGACAATTTG
-GT
->HWI-ST960:105:D10GVACXX:2:1101:12914:2190 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTATGTAA
-CAACTTTTCA
-TCT
->HWI-ST960:105:D10GVACXX:2:1101:12899:2205 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAAGAAAGT
-AGCATCAAAA
-CAA
->HWI-ST960:105:D10GVACXX:2:1101:12750:2211 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCATCTAGTA
-CATACTCTGT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:12962:2211 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTTTTGTC
-TGAGTACGAA
-CT
->HWI-ST960:105:D10GVACXX:2:1101:12876:2225 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTATAATT
-TTTAGTGAAT
-AAC
->HWI-ST960:105:D10GVACXX:2:1101:12908:2229 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATTATGAT
-GTAGAAGTAT
-TG
->HWI-ST960:105:D10GVACXX:2:1101:12760:2229 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTTGGGCT
-CTTGTTGTGA
-ATC
->HWI-ST960:105:D10GVACXX:2:1101:12926:2234 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTATTCAG
-CAGGATTATG
-CT
->HWI-ST960:105:D10GVACXX:2:1101:12942:2239 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTATTTCAT
-TGTCTTGTCG
-GT
->HWI-ST960:105:D10GVACXX:2:1101:12902:2246 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTTATTTA
-CATGTTGTTT
-GG
->HWI-ST960:105:D10GVACXX:2:1101:13052:2176 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCTTTGTGA
-CTGATCATTA
-G
->HWI-ST960:105:D10GVACXX:2:1101:13197:2180 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTTTGTCA
-CATTGTAAAT
-CCC
->HWI-ST960:105:D10GVACXX:2:1101:13235:2181 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTAATAAG
-ATTTTCTAGT
-TG
->HWI-ST960:105:D10GVACXX:2:1101:13099:2185 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TTCTCTGTAT
-CTCTCGACTC
-TCT
->HWI-ST960:105:D10GVACXX:2:1101:13082:2187 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTAGTATTA
-TTATACACAC
-TTG
->HWI-ST960:105:D10GVACXX:2:1101:13132:2192 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTATAAAT
-AAGCTTTGTT
-CA
->HWI-ST960:105:D10GVACXX:2:1101:13120:2196 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTAATTTG
-GACTGAGTCT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:13177:2199 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCACTACGTC
-GTTTTGTTCT
-CTC
->HWI-ST960:105:D10GVACXX:2:1101:13060:2203 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAATTAAAG
-AAGAACCCAA
-AAC
->HWI-ST960:105:D10GVACXX:2:1101:13106:2213 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTCGTAAAC
-TCATAAATAA
-AT
->HWI-ST960:105:D10GVACXX:2:1101:13215:2231 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCACTGTGTT
-GGCGTTTTAT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:13012:2238 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAAATGCCC
-ATTAATCGTG
-GT
->HWI-ST960:105:D10GVACXX:2:1101:13172:2240 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTGCCTAT
-TTATTTGCTG
-TC
->HWI-ST960:105:D10GVACXX:2:1101:13045:2241 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTCTGAG
-ATTGTAGAAC
-AAT
->HWI-ST960:105:D10GVACXX:2:1101:13155:2249 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCAAAAGGT
-CAAGGTTGGC
-AAG
->HWI-ST960:105:D10GVACXX:2:1101:13458:2176 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTATGTAAT
-GTAGTCTTTT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:13473:2178 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCGTTAGGAC
-AGTTC
->HWI-ST960:105:D10GVACXX:2:1101:13435:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTGAATAAT
-GAACTTTGAT
-TAA
->HWI-ST960:105:D10GVACXX:2:1101:13272:2183 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTAAATCT
-CCCTTTTTTT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:13312:2186 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTGTGTAG
-AATCTGCTTA
-TAA
->HWI-ST960:105:D10GVACXX:2:1101:13253:2186 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TAGTTTGGAC
-GTTGGTACAC
-GA
->HWI-ST960:105:D10GVACXX:2:1101:13363:2187 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTGCTAAGG
-AAGTAAAAGC
-CAT
->HWI-ST960:105:D10GVACXX:2:1101:13404:2208 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCACGACATT
-GCATTGTATG
-TTG
->HWI-ST960:105:D10GVACXX:2:1101:13366:2209 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTATATGTT
-GTCGGTTCTA
-GT
->HWI-ST960:105:D10GVACXX:2:1101:13340:2212 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAATATGTT
-TCGTAGAACT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:13430:2220 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTATGTTTT
-GGATACATAA
-AC
->HWI-ST960:105:D10GVACXX:2:1101:13478:2222 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCATGGTGAT
-GAAACGAATA
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:13253:2222 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTATGGGTC
-TCTAGATGCT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:13357:2234 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTGTCTTTG
-GTGCCCATGC
-AA
->HWI-ST960:105:D10GVACXX:2:1101:13444:2236 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTTTACGA
-TTCATGGTTC
-TGT
->HWI-ST960:105:D10GVACXX:2:1101:13383:2241 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATAATCTC
-TACTGTTTGT
-TCT
->HWI-ST960:105:D10GVACXX:2:1101:13323:2243 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATTCTCAA
-TACTTTCTTC
-CTC
->HWI-ST960:105:D10GVACXX:2:1101:13556:2177 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTTTGTAT
-AAACGGAATT
-TCT
->HWI-ST960:105:D10GVACXX:2:1101:13647:2177 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCTTGATCA
-CGAACATAAT
-ATT
->HWI-ST960:105:D10GVACXX:2:1101:13575:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAGCTTGCA
-AGTTCTCTCT
-GAA
->HWI-ST960:105:D10GVACXX:2:1101:13528:2185 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATAGTATG
-TTTGCGGATT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:13614:2188 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTTCTTTC
-GAGTTTTATG
-AT
->HWI-ST960:105:D10GVACXX:2:1101:13510:2190 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTGTCTTT
-CTCCTTCTCT
-TCT
->HWI-ST960:105:D10GVACXX:2:1101:13692:2200 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTGCTTTG
-CTTAATTCAT
-TG
->HWI-ST960:105:D10GVACXX:2:1101:13666:2203 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTCAAATTT
-CAATGAGATT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:13720:2208 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATCAGAGT
-GACTCAACCA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:13526:2209 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAGCCCTTT
-GTCGCTAAGA
-TTC
->HWI-ST960:105:D10GVACXX:2:1101:13506:2209 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAATAATGT
-GTGTGGGACT
-TA
->HWI-ST960:105:D10GVACXX:2:1101:13623:2212 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAATGGCAA
-TCGTCTCTCT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:13684:2220 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTATGGTC
-CCCACTGAGA
-ACT
->HWI-ST960:105:D10GVACXX:2:1101:13646:2224 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTTTGTTA
-TAGATTCCTC
-CT
->HWI-ST960:105:D10GVACXX:2:1101:13506:2227 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAGGAACAA
-GGATTACAAG
-AA
->HWI-ST960:105:D10GVACXX:2:1101:13700:2234 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTATAAGCT
-GAGCGAATAT
-TAG
->HWI-ST960:105:D10GVACXX:2:1101:13525:2242 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTGTTATT
-GGCCCAAGTA
-GA
->HWI-ST960:105:D10GVACXX:2:1101:13744:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTATGCTCT
-TTTAATGTGC
-AT
->HWI-ST960:105:D10GVACXX:2:1101:13514:2246 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTTTTCAA
-ACTGAGCAAA
-AAT
->HWI-ST960:105:D10GVACXX:2:1101:13631:2249 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAGTTAATG
-TCTCTGAAAC
-AA
->HWI-ST960:105:D10GVACXX:2:1101:13611:2250 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAACGTAGA
-AACTCTTGGT
-AA
->HWI-ST960:105:D10GVACXX:2:1101:13873:2169 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGGGGGTCC
-CAGTTCCGAA
-CCC
->HWI-ST960:105:D10GVACXX:2:1101:13832:2175 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTTGTGC
-CTTTTTCTCT
-TCT
->HWI-ST960:105:D10GVACXX:2:1101:13756:2181 1:N:0: bcd:RPI1 seq:CACATCACGATC
-CACATCACGA
-TCACAGTCGG
-CTTACCCGGG
-GAC
->HWI-ST960:105:D10GVACXX:2:1101:13888:2181 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTGAGAGA
-TTTCGTAAAA
-AAC
->HWI-ST960:105:D10GVACXX:2:1101:13863:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTTGGTTG
-GTGTAAAAAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:13978:2187 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTTGACTC
-TGTAGCTTTA
-CTT
->HWI-ST960:105:D10GVACXX:2:1101:13770:2198 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCAACATAT
-GTTTCATAAT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:13874:2204 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCATAAAAGT
-TGTCGTAGCA
-TAA
->HWI-ST960:105:D10GVACXX:2:1101:13985:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCTCTTGAC
-TTGCCTCCTT
-ACC
->HWI-ST960:105:D10GVACXX:2:1101:13941:2214 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGA
-TCTATTTATA
-TATTTGATGT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:13963:2214 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTCTGTCT
-ATTTCGTTAA
-ATC
->HWI-ST960:105:D10GVACXX:2:1101:13752:2222 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCTTTGTCAA
-TTGTCATATT
-TGC
->HWI-ST960:105:D10GVACXX:2:1101:13859:2223 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTCTGTTT
-CAATGTCCCT
-TGC
->HWI-ST960:105:D10GVACXX:2:1101:13939:2238 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAGAGTCAA
-GACTCAAGAC
-TAT
->HWI-ST960:105:D10GVACXX:2:1101:14180:2173 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCACAACAG
-CATATTTATA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:14103:2174 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAACAAAAG
-TGGCTGTAGT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:14196:2181 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTAGGTGT
-TACTGTGGAT
-TTC
->HWI-ST960:105:D10GVACXX:2:1101:14128:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTAATGTA
-GTAGCAACTC
-TT
->HWI-ST960:105:D10GVACXX:2:1101:14033:2191 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTGGTAA
-CTGGACTCTG
-AT
->HWI-ST960:105:D10GVACXX:2:1101:14074:2199 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTAATACA
-CTTTCCCTTA
-CAT
->HWI-ST960:105:D10GVACXX:2:1101:14019:2201 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCTCTCTGT
-GATTCTCTTT
-TTA
->HWI-ST960:105:D10GVACXX:2:1101:14232:2204 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAAGCTGGA
-AACTTTGAGC
-TT
->HWI-ST960:105:D10GVACXX:2:1101:14143:2204 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTTGTGG
-CACACTAAGC
-TG
->HWI-ST960:105:D10GVACXX:2:1101:14121:2210 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTCTAGTAG
-CATGTGAATT
-TA
->HWI-ST960:105:D10GVACXX:2:1101:14168:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTATTCTAT
-CGGATTCTCA
-AC
->HWI-ST960:105:D10GVACXX:2:1101:14102:2217 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTGTATTTG
-ATCTACATTG
-TAT
->HWI-ST960:105:D10GVACXX:2:1101:14036:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTCCCGAAC
-TCTACGTAGA
-AAT
->HWI-ST960:105:D10GVACXX:2:1101:14209:2227 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTACTCAA
-CACTCTCTTC
-TT
->HWI-ST960:105:D10GVACXX:2:1101:14087:2229 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTGAGTTCT
-TAGCCATTGC
-AT
->HWI-ST960:105:D10GVACXX:2:1101:14127:2230 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCACTCTGGA
-TTCAATTTGG
-AT
->HWI-ST960:105:D10GVACXX:2:1101:14472:2172 1:N:0: bcd:RPI1 seq:CACATCACGATC
-CACATAACGA
-TCCTCTGTGT
-CTCTCTCGAT
-CGA
->HWI-ST960:105:D10GVACXX:2:1101:14402:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAATAAAGT
-GGTCTAGTGG
-TT
->HWI-ST960:105:D10GVACXX:2:1101:14443:2185 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCTTTTACTG
-TCCTCTGATC
-AG
->HWI-ST960:105:D10GVACXX:2:1101:14420:2208 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTATGTAT
-ATATAAGAGT
-CAT
->HWI-ST960:105:D10GVACXX:2:1101:14467:2209 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTGAAACTG
-TACTTGAGAT
-TA
->HWI-ST960:105:D10GVACXX:2:1101:14311:2215 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTCTTTAT
-GGCTCTAGTA
-CAA
->HWI-ST960:105:D10GVACXX:2:1101:14442:2218 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAAAAATGT
-CGTTGTAGTA
-TAG
->HWI-ST960:105:D10GVACXX:2:1101:14388:2226 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAATTCCAG
-TTGATTGAGG
-TC
->HWI-ST960:105:D10GVACXX:2:1101:14404:2228 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTGTTGTTG
-GCTATGATGT
-TAT
->HWI-ST960:105:D10GVACXX:2:1101:14361:2234 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAAATTATG
-ATGGAAGATT
-TGT
->HWI-ST960:105:D10GVACXX:2:1101:14303:2235 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCACATTTAG
-GCTCAGTGGG
-A
->HWI-ST960:105:D10GVACXX:2:1101:14342:2235 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGCTCTTCA
-ACCTTAGAAG
-A
->HWI-ST960:105:D10GVACXX:2:1101:14263:2238 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTACTTTC
-TCGTGCTAAC
-TC
->HWI-ST960:105:D10GVACXX:2:1101:14512:2169 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGCAATCCC
-TCTGTTTCCT
-AA
->HWI-ST960:105:D10GVACXX:2:1101:14677:2181 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTGACAGA
-AGATAGAGAG
-CAC
->HWI-ST960:105:D10GVACXX:2:1101:14738:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAATGTTCA
-TGTCTAAATT
-CG
->HWI-ST960:105:D10GVACXX:2:1101:14684:2203 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAAGCCGGA
-GACAGGAGAG
-GTG
->HWI-ST960:105:D10GVACXX:2:1101:14526:2204 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCACATAGAC
-TAATCTTATA
-AT
->HWI-ST960:105:D10GVACXX:2:1101:14580:2206 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAAATAAGG
-TATCAGGTTT
-TA
->HWI-ST960:105:D10GVACXX:2:1101:14592:2223 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTTATAGG
-GAGAAGAAGA
-GGC
->HWI-ST960:105:D10GVACXX:2:1101:14659:2235 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAATTGGTG
-CCTGTAGGTC
-AG
->HWI-ST960:105:D10GVACXX:2:1101:14548:2237 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCAATTTTAT
-GTCGTTTCTT
-TG
->HWI-ST960:105:D10GVACXX:2:1101:14962:2168 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAATCCACA
-CTAAGTCCAA
-GC
->HWI-ST960:105:D10GVACXX:2:1101:14851:2171 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTATTTGTA
-GCAATTCTGT
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:14982:2172 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCGTAATCTG
-GGATGAACTC
-ACT
->HWI-ST960:105:D10GVACXX:2:1101:14927:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATTCTTGT
-TTAGAAGCAA
-GAA
->HWI-ST960:105:D10GVACXX:2:1101:14906:2195 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGCCAACTC
-TGTTTCTTCT
-TCT
->HWI-ST960:105:D10GVACXX:2:1101:14858:2195 1:N:0: bcd:RPI3 seq:CACTTAGGCATC
-CACTTAGGCA
-TCATTCGTTT
-CAATGTCAAT
-CTC
->HWI-ST960:105:D10GVACXX:2:1101:14936:2201 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAGCCAATG
-TTGTAGAACT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:14780:2204 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTTGTGAA
-TCCTTTTCCA
-TT
->HWI-ST960:105:D10GVACXX:2:1101:14808:2217 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAATGAAGA
-GGCTGTTTCT
-AC
->HWI-ST960:105:D10GVACXX:2:1101:14828:2217 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATGTATGT
-TGTTATTTGA
-TAA
->HWI-ST960:105:D10GVACXX:2:1101:14929:2217 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAACACTCT
-TATCAAAAAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:14844:2223 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCATACATCT
-TTGCAGAACT
-CAT
->HWI-ST960:105:D10GVACXX:2:1101:14988:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAGCTTAGA
-CTTGGTAGTT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:14821:2236 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAGTGTACT
-TGTGGACAAG
-GT
->HWI-ST960:105:D10GVACXX:2:1101:14761:2243 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATTTGTAG
-TCGTAAATAT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:15030:2168 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTCTGTTA
-CACGCCGAGA
-TC
->HWI-ST960:105:D10GVACXX:2:1101:15079:2180 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTCAGGGCA
-AGCACAACAT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:15143:2186 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCATCTTTTT
-CATCCCAATC
-TGT
->HWI-ST960:105:D10GVACXX:2:1101:15178:2193 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAGTGATGA
-ACCTTTTGAA
-CC
->HWI-ST960:105:D10GVACXX:2:1101:15053:2195 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAATCCAGT
-CTCATCGCTG
-TTG
->HWI-ST960:105:D10GVACXX:2:1101:15025:2214 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGA
-TCGTATGTAA
-AGGTTTACTC
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:15186:2216 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCAGAGCAAG
-TCGAAATCTG
-TT
->HWI-ST960:105:D10GVACXX:2:1101:15065:2224 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTGTGCTG
-GGAACTATTT
-GAC
->HWI-ST960:105:D10GVACXX:2:1101:15143:2225 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATGAAAAC
-TTCTTGAGTT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:15008:2227 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCTTTCTTGG
-GACTTGATTT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:15207:2236 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTAGTGT
-GTAATGTTAT
-TGG
->HWI-ST960:105:D10GVACXX:2:1101:15000:2247 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTTGGTCA
-TGTTTGCTAT
-TTG
->HWI-ST960:105:D10GVACXX:2:1101:15274:2198 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCATCTGTC
-TAAAGTTTGT
-TCT
->HWI-ST960:105:D10GVACXX:2:1101:15308:2216 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAGTAATTT
-AGCATGTTGC
-AAA
->HWI-ST960:105:D10GVACXX:2:1101:15475:2222 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTCTGTAG
-TTGTATTTCA
-AC
->HWI-ST960:105:D10GVACXX:2:1101:15291:2232 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTATGTTG
-TTAGCTATCA
-CT
->HWI-ST960:105:D10GVACXX:2:1101:15347:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTGAACTCT
-GACCAATGAA
-CTT
->HWI-ST960:105:D10GVACXX:2:1101:15331:2245 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTGTTATA
-TATTACTGAC
-TAC
->HWI-ST960:105:D10GVACXX:2:1101:15450:2248 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTGTTTTGT
-CCCTTTGTAT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:15691:2179 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTACTAGTC
-TCGTATTAAC
-TA
->HWI-ST960:105:D10GVACXX:2:1101:15591:2179 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTTTGCTT
-ATGTGCCCGT
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:15612:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATATCCTA
-TGTCTAAAAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:15528:2190 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCATTTCGGA
-TCTTGGCTAC
-TAA
->HWI-ST960:105:D10GVACXX:2:1101:15503:2198 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAATCTAAA
-GGGATTTGGT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:15541:2201 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CAAACTTGAA
-TCGTCTGTAG
-CTCTAGACCA
-TTC
->HWI-ST960:105:D10GVACXX:2:1101:15700:2204 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTAAATTC
-TCTTCCTTTG
-GT
->HWI-ST960:105:D10GVACXX:2:1101:15649:2217 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTAATGTGA
-TGGTTTCTTC
-AA
->HWI-ST960:105:D10GVACXX:2:1101:15573:2222 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAATAGCTA
-GTCATAACTC
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:15731:2236 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAATATGTT
-TCGTAGAACT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:15639:2244 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCTTTTACG
-GAGTACAAGA
-GAT
->HWI-ST960:105:D10GVACXX:2:1101:15824:2174 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTATATGTC
-TGTACACAAT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:15924:2187 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTATGAAA
-ATGTTGTGAA
-CTG
->HWI-ST960:105:D10GVACXX:2:1101:15857:2189 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCTTAGGTT
-TAGAGCTAAA
-AAA
->HWI-ST960:105:D10GVACXX:2:1101:15755:2216 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTATACTA
-CTAATACATT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:15970:2220 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCCATGACTG
-AAGTTGTTTG
-TC
->HWI-ST960:105:D10GVACXX:2:1101:15886:2223 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTTGTTTT
-ATTTCTTATT
-CAA
->HWI-ST960:105:D10GVACXX:2:1101:15866:2238 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCTGTGTTG
-GCGTTTTATC
-TG
->HWI-ST960:105:D10GVACXX:2:1101:15925:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTTTTGTT
-GGATTGTTTT
-GCT
->HWI-ST960:105:D10GVACXX:2:1101:15938:2248 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTCTTGTCC
-GTTACATTTG
-CC
->HWI-ST960:105:D10GVACXX:2:1101:16016:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCACTGTGTT
-GGCGTTTTAT
-CTG
->HWI-ST960:105:D10GVACXX:2:1101:16084:2189 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAAATGTGA
-AATCTTAAAA
-TC
->HWI-ST960:105:D10GVACXX:2:1101:16060:2193 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCGAGAATGA
-TGAACCAATT
-AC
->HWI-ST960:105:D10GVACXX:2:1101:16022:2204 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCATGAGAT
-ACTGAATTCA
-AGC
->HWI-ST960:105:D10GVACXX:2:1101:16131:2207 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTATGTAT
-GATCATATTT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:16147:2216 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCATTCAAAT
-CAGAGGCTTG
-TTA
->HWI-ST960:105:D10GVACXX:2:1101:16171:2218 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTCTTCTTC
-GTTTGGCTAT
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:16114:2220 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTGCAGCAC
-TTGTCTGACC
-CAT
->HWI-ST960:105:D10GVACXX:2:1101:16083:2223 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAATGTAGA
-GAATCGATTT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:16174:2241 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCACTTTGAG
-AACTAAAAAA
-AA
->HWI-ST960:105:D10GVACXX:2:1101:16002:2242 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTGGAGTTT
-TGGTTAGGTT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:16214:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTTGGTAG
-ATGATAACAA
-ATC
->HWI-ST960:105:D10GVACXX:2:1101:16126:2245 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATTGTTGT
-TGTTGTTGTT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:16191:2247 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCTGGAGAAC
-TTGGCAACTC
-AC
->HWI-ST960:105:D10GVACXX:2:1101:16438:2169 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATGTTCGG
-TTGTGGGATT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:16355:2177 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTTGTTA
-GACTCTTCGA
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:16306:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTACCTACT
-CGTCGTACAT
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:16427:2183 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGTTGATTT
-TAATGGTTAC
-TGT
->HWI-ST960:105:D10GVACXX:2:1101:16368:2191 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATAAAAAC
-TCTGAATTTA
-AT
->HWI-ST960:105:D10GVACXX:2:1101:16496:2191 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTTCTGTTG
-AACCTCTTG
->HWI-ST960:105:D10GVACXX:2:1101:16268:2194 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTCAAACC
-ATTGAGACAG
-CTT
->HWI-ST960:105:D10GVACXX:2:1101:16478:2197 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCCTGTGAAA
-CTGCGAATGG
-CT
->HWI-ST960:105:D10GVACXX:2:1101:16378:2215 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTACGTTA
-TTTAAAATCC
-TC
->HWI-ST960:105:D10GVACXX:2:1101:16273:2227 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTGTTATGT
-GACTGGAGAG
-A
->HWI-ST960:105:D10GVACXX:2:1101:16350:2227 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTGTGGCT
-CAGAACCACC
-AC
->HWI-ST960:105:D10GVACXX:2:1101:16328:2230 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAA
-TCACTGATCG
-CGTCGTGTTA
-C
->HWI-ST960:105:D10GVACXX:2:1101:16408:2232 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTTCGAAC
-AATGAACAAT
-TGC
->HWI-ST960:105:D10GVACXX:2:1101:16369:2234 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTACATTGT
-GAAATGATAT
-TTC
->HWI-ST960:105:D10GVACXX:2:1101:16305:2250 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCAAACCTG
-TATCTGTGTA
-ACT
->HWI-ST960:105:D10GVACXX:2:1101:16647:2170 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTAATTGAA
-TATCTTCAAT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:16734:2178 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTACGAAT
-TCTAAATTTT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:16682:2192 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTATCAATA
-AGCGGAGGAA
-AAG
->HWI-ST960:105:D10GVACXX:2:1101:16516:2203 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGAGAGTTC
-GAATCTGTCA
-GGC
->HWI-ST960:105:D10GVACXX:2:1101:16583:2204 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATCGGCGC
-TTGTTCACCT
-CTC
->HWI-ST960:105:D10GVACXX:2:1101:16633:2220 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCATTGTATT
-TTAACAGCAC
-TC
->HWI-ST960:105:D10GVACXX:2:1101:16696:2231 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTATGTAAT
-GTAGTCTTTT
-AT
->HWI-ST960:105:D10GVACXX:2:1101:16666:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCTTAACAC
-TTGGTTCCGT
-TTC
->HWI-ST960:105:D10GVACXX:2:1101:16730:2240 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCCTATAAA
-TCGTCTCATG
-AA
->HWI-ST960:105:D10GVACXX:2:1101:16561:2240 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATAACCCT
-TTCCAGGCCA
-TGT
->HWI-ST960:105:D10GVACXX:2:1101:16708:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCACCATTG
-TCTGAATAAA
-AAG
->HWI-ST960:105:D10GVACXX:2:1101:16847:2173 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCGATGTCGG
-CTCTTCCTAT
-CAT
->HWI-ST960:105:D10GVACXX:2:1101:16809:2177 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCACATCCTC
-ATAATCACTT
-TC
->HWI-ST960:105:D10GVACXX:2:1101:16946:2180 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTCTTTTG
-TCGGCGTTAG
-GT
->HWI-ST960:105:D10GVACXX:2:1101:16831:2183 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTATGTTAT
-GGATTCAAAA
-AAA
->HWI-ST960:105:D10GVACXX:2:1101:16770:2187 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTCAGCCCT
-TTGTCGCTAA
-GA
->HWI-ST960:105:D10GVACXX:2:1101:16858:2188 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAATTTTTA
-GTGACCCTTT
-TA
->HWI-ST960:105:D10GVACXX:2:1101:16876:2193 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTATGTTC
-TCTGTTATTC
-TC
->HWI-ST960:105:D10GVACXX:2:1101:16983:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCCTTTGTGG
-GTTGAGTTGT
-CT
->HWI-ST960:105:D10GVACXX:2:1101:16842:2205 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTATGAAA
-TCGACCATGA
-CA
->HWI-ST960:105:D10GVACXX:2:1101:16962:2210 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTCATGCT
-GTTTTCCAAC
-AGC
->HWI-ST960:105:D10GVACXX:2:1101:16751:2219 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTACTGTT
-TTCTGTTTTC
-TT
->HWI-ST960:105:D10GVACXX:2:1101:16898:2223 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCAACCCCCG
-AACTATATCC
-TC
->HWI-ST960:105:D10GVACXX:2:1101:16969:2228 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCATTATCTT
-GTAGAATGTT
-CA
->HWI-ST960:105:D10GVACXX:2:1101:16781:2240 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTTCTCCT
-CTCGTCCATA
-AAT
->HWI-ST960:105:D10GVACXX:2:1101:17222:2169 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTGGATCCT
-GTTTTGGATT
-GT
->HWI-ST960:105:D10GVACXX:2:1101:17028:2180 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATA
-TCCTATTTAC
-TATTTGAAAA
-AGC
->HWI-ST960:105:D10GVACXX:2:1101:17127:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCAATTGGAC
-TGTTTAACGT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:17143:2189 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCAAATTTCT
-ATATATTGTT
-TT
->HWI-ST960:105:D10GVACXX:2:1101:17161:2201 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCTTCTGGAC
-ATTAGCCATT
-AGT
->HWI-ST960:105:D10GVACXX:2:1101:17133:2206 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCTGCCTTTT
-CCTTCTTGTC
-GG
->HWI-ST960:105:D10GVACXX:2:1101:17121:2224 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGGCACTTC
-TGTTCTGATC
-CT
->HWI-ST960:105:D10GVACXX:2:1101:17033:2228 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCACTAGACA
-AACTCTCAAG
-A
->HWI-ST960:105:D10GVACXX:2:1101:17178:2238 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGTTTGTAG
-TCATAATTTA
-GT
->HWI-ST960:105:D10GVACXX:2:1101:17141:2241 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGA
-TCGTATGTTT
-CACTCTGTAA
-CT
->HWI-ST960:105:D10GVACXX:2:1101:17119:2246 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCGAGACCAG
-ATGTGCGATG
-TTT
->HWI-ST960:105:D10GVACXX:2:1101:17246:2247 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAA
-TCATTTGGTT
-AGGTCCTTTG
-TTC
->HWI-ST960:105:D10GVACXX:2:1101:17011:2248 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTTTTGAGG
-TTTTAAGATG
-TT
->HWI-ST960:105:D10GVACXX:2:1101:17469:2169 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCA
-TCTGTGTTGG
-TGAAGGAAGG
-AAC
diff --git a/src/libqes/test/data/test.fastq b/src/libqes/test/data/test.fastq
deleted file mode 100644
index c66fd84..0000000
--- a/src/libqes/test/data/test.fastq
+++ /dev/null
@@ -1,4000 +0,0 @@
- at HWI-ST960:105:D10GVACXX:2:1101:1151:2158 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAANGACATTGAATCTATATGT
-+
-JJJJJJJIJHIJCC#4ADFFHHHGHJJJJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1205:2165 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTGNATTCTTCTTTTGGAACTC
-+
-JIJIJJJJJIIIBC#4ADDDHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1122:2186 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCAGTTTAAAGTTAACTCATTG
-+
-JIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1229:2187 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTGAGTTTTTGGACTGTACAT
-+
-IJJJJJJJJJJJCCCFFDFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1175:2195 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTAATTGTCACTGTTTCACCC
-+
-IJJHHIJJJJJJCB at FFFFFHHHHHJJJJJIGJ
- at HWI-ST960:105:D10GVACXX:2:1101:1175:2224 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTGTGACTCTGTTCCTGTTGT
-+
-IJJJJJJJJJJJ at BCFFFFFHHHHHIJJIIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1204:2232 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATCACAGAGCAGCAGTATTTC
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJHIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1237:2239 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTACACACGTATATGCAATAC
-+
-IJJJJJJJJJJICCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1123:2239 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAATAATGTGGTATTAGTCTG
-+
-JJJIJJJJIJJJBCCFFFFFHHFHHJIJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1155:2246 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAGCCACTGAACTAAAAAAAAA
-+
-HFFFFFEEEEEECCCFFFFFHGHHGJJJJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1466:2165 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTGNAAACGCATGTAGATGAT
-+
-JJJJJJJJJJJJCC#4ADFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1443:2173 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTACCAAAGTCTGAATGATTAT
-+
-IJJJJJJJJJJJCCCFFFFFHHHHGJIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1360:2176 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCCGGCTCTGTCTCTCTCTCCC
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1272:2183 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATCATTTAGAGGAAGGAGAA
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJIIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1423:2185 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTATGACGTCAAATTATGCCT
-+
-JIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1398:2186 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAAAAAAAAAAAGAATAAAGAA
-+
-C at CBBAABCCCC@@@DDDDDHHFDFIBFHG<FH
- at HWI-ST960:105:D10GVACXX:2:1101:1333:2199 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTATTACAAAGTTTACATCTCT
-+
-JJJJJJJJJIJJCCCFFFFFHHHHHJIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1388:2214 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTCGTCTTCCATTTCTATTT
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1366:2229 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTATGTATATGCTGTGGTAG
-+
-JIIJJJJJJJIJCBCFFFFFHHHHHJIIJFFG
- at HWI-ST960:105:D10GVACXX:2:1101:1297:2232 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCATTCATGTTGATATATTTAT
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1374:2245 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTGTGTGTCTGAAGTAGTTGA
-+
-IIIIGIIJJJJJ@@CFDDFFHHHHFJGIIIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1277:2249 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATGTTTCAGACTTCGAGAAGC
-+
-JJJJJJJJJGIHCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1425:2250 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTATATACTTCACAACTCTG
-+
-JJJJIIJJJJJJCCCFFFFFHHHHHJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:1714:2160 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTNGTATGAACTCTGGTTTA
-+
-JJJJJJJJHJJJ@@#4ADDFHHHHHJJJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1601:2174 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGATCTTTTACGTAGACGATGTGCC
-+
-IGJJJJJCDHGICCCFFFFFHHHHHIJIIGIJ
- at HWI-ST960:105:D10GVACXX:2:1101:1581:2174 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCAGTTGAGGAACTATTGTTTC
-+
-HIJJIIIJIIIJCCCFDFFFHHHHHJJJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:1717:2186 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCAATCTTTGTACTGTTGAACAA
-+
-HIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1538:2187 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAACTGTTTGTGTCAATCATT
-+
-JHJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1687:2195 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTGTCCTTCGGATCACTCAA
-+
-IGIIJJJJJJJJCCBFFFFFHHHHGJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1589:2195 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTGAGCACAAAGATGATCAAAC
-+
-JJJJJJJIJJJJCCCFFFFFHHGHHJJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1611:2205 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTGAGAGTAGCTCTGTTTAT
-+
-IJJJJJJJJJIJCCCFFFFEHHHHHJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:1672:2207 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTATATTTGATACATCGGTTC
-+
-IIJJJJJIJJJJCCCFFFFFGHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1595:2220 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTCTGACTGATGAACATATTT
-+
-IDHIIJJIJEIGCCCFFFFFGFHGFHIIIGIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1706:2224 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTGTGCAATTAGTGCAACTGA
-+
-JJJJJJJJJJJJCCBDFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1575:2228 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCGTTTGAGACTCTATCTTACCT
-+
-JJJJJJJJJJJJ at CCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1557:2229 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATTTTTGTGTGTACTTGTCC
-+
-IGIJIGIJGGGH at CCFFFFDHDHHHJIJGHIJ
- at HWI-ST960:105:D10GVACXX:2:1101:1747:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTATATACAATTGTGGACTAC
-+
-IIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1835:2159 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTNAGTTTCTTCTTCATTGT
-+
-JHJJJJJJJJJJ at B#4ADDFHHHHHJJJJJIG
- at HWI-ST960:105:D10GVACXX:2:1101:1976:2160 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCACNAGGTCGAATCGAAATGT
-+
-HAHIIJJIJJIH@@#4ADADDHHHHIIJJJII
- at HWI-ST960:105:D10GVACXX:2:1101:1781:2164 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTNTGTGTTGTTGACTCTGT
-+
-JJJJJJJJIJJJCB#4ADDDHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1903:2165 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATNATCAGAGACTAAAGTAGT
-+
-IJJJJJJJJJJJ at C#4ADDDHFDHHJGIGEIGH
- at HWI-ST960:105:D10GVACXX:2:1101:1854:2165 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATNATATCCTACTACAATGC
-+
-IIIFBGDGCGII@@#4ADD=FHDHHGIGIIII
- at HWI-ST960:105:D10GVACXX:2:1101:1756:2166 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATNTGGTCGATATGTCTTTT
-+
-HGJJJJJJJHHHBC#4ADDFHHHHHJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1921:2172 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTTTTAGAACTCTTTTCCTA
-+
-FHIIB8CHGIII@@<DDD?DH??FFEDHGC@@
- at HWI-ST960:105:D10GVACXX:2:1101:1992:2192 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTTGTTGGGGTAAAAAAAAA
-+
-@@CE@?BCACDCBCCFFFFFHH at FHJJJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1925:2197 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTAAGTGTGATTCTTTTGG
-+
-GDHIEHJJGEGH@@BFFBDEHHHGHIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1792:2234 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTAAAGTCATGTCTTTGTTGT
-+
-HIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1771:2239 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGGTGACCGAGAAATGTTTAA
-+
-IIIIIIIIIIFF@?@DDDDD?CCF:EGG at G@D
- at HWI-ST960:105:D10GVACXX:2:1101:1915:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTCAGTCTAACTAAAGTATT
-+
-IJJIJJJJJJJJ@@BFFDEFHHHHHJJJFHJJ
- at HWI-ST960:105:D10GVACXX:2:1101:1899:2246 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCACTAATACAATTGTTGCTC
-+
-JJJJJJJJJJJJ at CCFFFFFHHHHHGHGHHII
- at HWI-ST960:105:D10GVACXX:2:1101:2023:2160 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTANAATTGTGTGTAAAGTAA
-+
-IJJJJIJJJJJJ@@#4ADDFHHHHFHIIJHIJ
- at HWI-ST960:105:D10GVACXX:2:1101:2059:2162 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTANTGGGAACATAAATGAAGG
-+
-FCFAEFHGCEAC@@#4ABBDHDHFFFHIGIIIH
- at HWI-ST960:105:D10GVACXX:2:1101:2077:2163 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTNGGTTCCGAGGCCCTCTC
-+
-@=CAHHEFFFFC@@#4AABDHHFHFIGIIGIG
- at HWI-ST960:105:D10GVACXX:2:1101:2182:2164 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTANCTTCTCTGTTATGTCTC
-+
-JJJJJJJJJJJJCC#4ADFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2049:2181 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGTTCTTGTACTACAGTGAT
-+
-HGIFGGCDFGIH:??DBDDBFBFDHGIEADCI
- at HWI-ST960:105:D10GVACXX:2:1101:2035:2185 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATGTAGAATTCAGAATGTCT
-+
-IIJJJIJJJJJJCCCFFFFFHHHHHJJJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2214:2203 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCTGTACACGGCTTAATTTATT
-+
-JJJJIJJJJJJJCCBFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2244:2217 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCGGTTTGAGTGTTGCAAATCT
-+
-==BCC at C@D at 77??<A?D?BC2<DDCEEEE at BF
- at HWI-ST960:105:D10GVACXX:2:1101:2185:2223 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCAACAAGGTCGTTGTAGTATAG
-+
-IJJJJJJJJJJJCCCFFFFDHHHHHJJJIIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2067:2226 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATTCCATAGATTGTAGCCTC
-+
-IGIJJJJJJJJJCCCFFFFFHHHHHIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2032:2227 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTTTGTTAGTTACGCTTTGC
-+
-JIIIJJJJJJJJCBCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2011:2230 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTAATATGATATGAAAATCT
-+
-JJJJJJJJJJJJCBCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2444:2173 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTTCCTGTGATTTGCAATTTC
-+
-HJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2254:2194 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCCATAAAAAGTCTCTACAAT
-+
-JJJJJJJJJJJJCCCFFFFFHHFHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2448:2203 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAGAAGAAAAAGATGACCAGCT
-+
-HIJJJIIJJJJJCCCFFFFFHHHHHIJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2342:2213 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAATGTTCGACTGTGAACCTTC
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2268:2215 1:N:0: bcd:RPI3 seq:CACTTAGGCATC
-CACTTAGGCATCAATATCAGAACTCGTTATATT
-+
-IJJJJJIIJJJJBBCFFFFFCDFFHJHIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2411:2223 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGATCGCAACTGTAGCAAGAAGAAAC
-+
-GIJJJJJGIJJICCCFFFFFHHHHHJJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2292:2229 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTTTACTTAAAGAGCCCTAAC
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:2448:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATGAGTGTAGGCTTACTTAC
-+
-HIJJJJJJJJJICCCFFEFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2389:2235 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTCGATCTGGTTTGTAGAAC
-+
-IIJJJIJJJJJJCCCFFFFFHHHHHJHIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2607:2158 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTNAACCTGTAGTAATGAAG
-+
-IJJJJJJJJJJJCC#4ADFFHHHHFHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2633:2162 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAGNATGAACTCATGAACTTTT
-+
-HIJJJJJJJJJHCC#4ADFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2513:2166 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTANGTAATGTAGTCTTTTAT
-+
-JJJIIJJJJJJJCC#4ADDFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2675:2178 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTAAGTGAACTCTGTGCGTCT
-+
-JIJJJJJJJJJJCCCFFFFFHHHHHJJJJJHIJ
- at HWI-ST960:105:D10GVACXX:2:1101:2548:2190 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAATCTTCTGTTGACTCATGT
-+
-JIJIHJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2610:2203 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTAGTATCAATTGAACTTTT
-+
-IJJJJJJJJJJJCBCFFDFFHHHHHIJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2657:2203 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCATATATATATAAATGCAGAC
-+
-FHJJJIJJJJJJCCCFFFFFHHHHHJJIIJIII
- at HWI-ST960:105:D10GVACXX:2:1101:2576:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATATTTTTCCCACTGTGTTCT
-+
-HIJJJJIJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2626:2215 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGAGAACTCTAGAAACCTGCTT
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2660:2219 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTCTACAATGTACTGGAAACTT
-+
-JJJIJHEEGIII@@@FFFFEFFDDDFGHGHIGI
- at HWI-ST960:105:D10GVACXX:2:1101:2509:2223 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTCAAACTTTATGTAAACTCT
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2536:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCATACCAAATAGAATTTCTG
-+
-HIJIGHEGGIGACCCFFFFFHHHHFFHGJJII
- at HWI-ST960:105:D10GVACXX:2:1101:2584:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTGTGCCTGGATTAATATGA
-+
-IJJJIJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2674:2235 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATGCAACTGCAAATTCTGCA
-+
-IIIJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2718:2235 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCACGGAACCAGTGACCGTCGT
-+
-IIJHHGHHHHHFCCCFFFFDHHHHHJIEIIIJ
- at HWI-ST960:105:D10GVACXX:2:1101:2630:2245 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTACTTGAACAGGATCTGTT
-+
-?FGBGECHEHE9111442=BFFHHHHGEADDA
- at HWI-ST960:105:D10GVACXX:2:1101:2808:2165 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCACNTGTGATTGTAGTCATGT
-+
-IHJIJJJJJJJJCC#4ADDFHHHHHJIIJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:2922:2166 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCTNACTGGCGGCGAGAATAT
-+
-DDDDDDDDDDDDBC#4ADDFHHHHHJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:2869:2185 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCTCCGATGATGATCAAATCAT
-+
-HJJJJIJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2917:2207 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAAGTCTCGCTTATGACTATGA
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2789:2236 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATATTGGTCTGTATTGTGCTC
-+
-FGIIJGIIIIJIC at CFFFFDHHHHHHIJHIIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:2841:2242 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAAGAACTAACAGATATATGT
-+
-IEIJJJJJJJIJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3131:2158 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATNGACTTAACAAGTTGGTCT
-+
-IJJJJJJJJJIJCC#4ADFFHHHHHJHIJJGIJ
- at HWI-ST960:105:D10GVACXX:2:1101:3006:2164 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTNTTCAGCTACATGCTGAC
-+
-IJJIJJJJJJJJCB#4ADFFHHHHHJFIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3043:2167 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGANAAGAACCAAAACTATAA
-+
-JJJJJJJJJJJJCC#4ADDFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3188:2167 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAANAGTGGTGGATTAGTAGT
-+
-JJJJJJJJJJJJBC#4ADDFHHHHHJJJHIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3211:2194 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTATGTAATGTAGTCTTTAAA
-+
-JJIJJJJJJJJJCCCFFFFFHHHHHIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3145:2195 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTGGCTGTGGAGTAAAAAAAA
-+
-HFHHDFFFDEEE at CCFFFDFHHHDHEHIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3082:2195 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCACTGTGTTGGCGTTTTATCT
-+
-JIJJJJJJJJJHCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3160:2208 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCACTTGTTGGCCAAAAAAAAA
-+
-FFFFFEEEEEEECCCFFEFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3135:2214 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCGACAGGAGAGGTGATCGGAGT
-+
-############?=?D;2=2CDB22C:<A:??F
- at HWI-ST960:105:D10GVACXX:2:1101:3213:2220 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTGTTCTGTTGAAGGAGCTTTT
-+
-HIJJJHIJJIHHBC at FFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3036:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTATATACTTCACAACTCTG
-+
-IJJJJJJJJJJJCCBFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3140:2228 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAGCAAATAAGTCAAAACTTT
-+
-HGHIGGHHHIGIB at CFFDDDFHFFHJJIIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3106:2228 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCTTAGCTCGACCTAACACTT
-+
-IIJJJJJHHHHHCCCFFFFFHHHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3085:2237 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCTCATCAACTTTGTCTCTGCTT
-+
-HJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3151:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAATTCCATGTACTTACATTCC
-+
-JJJJJJJJIIJICCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3041:2247 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTGTAATACCTTTTATATATAG
-+
-IJJJJJIDHIJJCC at FFFFFHHHHHJJJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:3218:2248 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAGCCCAAACTGCATGCACAT
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3400:2159 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTNGAACTCTTCTTGGCTGC
-+
-JJJJJIGEGIIJCC#4ADDFHHGHGIIIIIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3487:2160 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTNGACATATATCAACTTTAC
-+
-HIJJJJJJJJJJCC#4ADDFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3325:2162 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTNATATTTCGTTGGACTGT
-+
-IJJIIJJJJJJJCC#4ADFFHHHFHIIJJIIJ
- at HWI-ST960:105:D10GVACXX:2:1101:3342:2163 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTNGTTACTTTGATCCTGAA
-+
-IJJJIJJJJJJJCC#4ADDFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3432:2166 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGCNCTGTGATTGCTTCGCCT
-+
-JJJJJIJJJJJJCC#4BDDDHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3370:2167 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATNTCAAAGTGTTTCTTTGTT
-+
-HIJJJJJJJJJJCC#4ADFFHFHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3440:2193 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTTGGATTGAAGGGAGCTC
-+
-HIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3302:2194 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCAAGTCATGACTCATGAGCTA
-+
-FHIJJIJIJJJJCCCFFFFFHHHHHJJJJJJII
- at HWI-ST960:105:D10GVACXX:2:1101:3369:2202 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATTGTCATATTTGCGATGTAT
-+
-HJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:3257:2202 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTATGTAAACTCTCGTGTGGCT
-+
-FHIIIGIJIJJHCCCFFFFFHHHHHJHJHIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3285:2210 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTGAGATGCAAAACAGTAGTTT
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJHIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3316:2236 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTAAATCTTAATCTCAAAT
-+
-IGIIIIIJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3555:2158 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTNGTAATCTGACTCTCTTT
-+
-IJJJJJJJJJJJCC#4ADDFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3609:2161 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAANGTTATGTTCTGGACCTAA
-+
-HEHHIHCHGIIICC#4ADDFHHHGGIIEHGIII
- at HWI-ST960:105:D10GVACXX:2:1101:3629:2162 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTNTTATGTAGAACTAAGAT
-+
-JJIEFIJJIIIJCC#4ADDFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3522:2164 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTNAGTTCTTTTGTGCCTTC
-+
-JJJJJJJJJJIJBB#4ABDDHHHHHHIJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:3597:2170 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTCCCCCGTGAGTTACTTCAC
-+
-HIIGG at ADHHHH@@?ADDDDCFHDHGIBGEGH@
- at HWI-ST960:105:D10GVACXX:2:1101:3651:2176 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTATATGTAGGCTAAAAAAAAA
-+
-HEEDFFFFEEEEC at CFFFEFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3568:2179 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTATTTATGTTTTGGACTTGT
-+
-HGHIJJJJJJJJCCCFFFFFHHHHGJIJJJIH
- at HWI-ST960:105:D10GVACXX:2:1101:3545:2181 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATGTGTGTTGTGGTTTTTAT
-+
-FCHIIIGIIHIG@@@ADBDDFHFFHFHGIIJG
- at HWI-ST960:105:D10GVACXX:2:1101:3669:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCACTGTGTTGGCGTTTTATCT
-+
-JJJJJJJJJJJHCCCFFFFFHHGHHGIJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3587:2184 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTAAGTGTAGAATGCATACAA
-+
-IJJGJGIIIJJJCCCFFDFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3570:2218 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGTTGTATGATTGAAGAAAT
-+
-JJJJJJJJJJJJCCBFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3530:2235 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTAACGAAAACTATTTAAAAT
-+
-HIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3706:2247 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAAGGCGAGTGTATCTCAACAA
-+
-IJJGHIHGHHHF at CCFFFFFCFDDHHIGIHHGJ
- at HWI-ST960:105:D10GVACXX:2:1101:3809:2165 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAANCTGTAGTTTTCCTTCCTT
-+
-IJJJJJJJJJJJCC#4ADDFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3872:2165 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTGNGGTAGATATGAGGTTAA
-+
-JIJIJJJIJJJJCC#4ADDFHHHHHJJJHIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3775:2173 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTACATTAAGGCAGTTCATTG
-+
-IJJJJJJJJJJJCCCFFFFFGHHGHJIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3902:2188 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTCACAAATGAACTTAAACT
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3885:2192 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTACCTACTCGTCGTACATTTT
-+
-==CCDCEE??AA@;@DDDDDAHDHFIIGGE at HH
- at HWI-ST960:105:D10GVACXX:2:1101:3807:2204 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCATCTCGGACCAAAGAGAGC
-+
-JJJJJJIJHHHHCCCFFFFFHHHHHJJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:3780:2206 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTGCATGTTGTGCACCGGCTCC
-+
-GHJIHHHHFFFFCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3853:2215 1:N:0: bcd:RPI3 seq:CACTTAGGCATC
-CACTTAGGCATCTCCGATGATGATCAAATCAT
-+
-JJIGGIIJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3946:2218 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTAGTCTTTTGGTATTTTA
-+
-JJJJJJJJJJJJCBCFFFFFHHHHHGHIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3976:2221 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATTGTTCGGCTTTGGATTAAG
-+
-IJJJJJJJJJJHCCCFFFFFHHHHHJJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3866:2227 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAATACGATATGTATATGTAC
-+
-JHJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3816:2234 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTAGGTCTTGTGTAGAAACT
-+
-JJJJJJJJJJJJCBCFFEFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3779:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTTTGAGTTTCGAGTTATCTG
-+
-JJJJJIJJJIIICCCFFFFFHGHHHJHIIJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3799:2247 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATTCTATCTACTACTTTTTC
-+
-JIJJJJJJJJJJ at BCFFFFFHHHHHIJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:3759:2247 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAACTAGTATAGTCAGAAAAT
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:3912:2249 1:N:0: bcd:RPI3 seq:CACTTAGGCATC
-CACTTAGGCATCATGTGAACAAGAACATATCCT
-+
-IJIJHIHJJJJJCCCDFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4038:2162 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCGTNGATTGAGGTCGGCAACAT
-+
-JJJIHHHFFFFFCC#4ADFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4099:2173 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCTTGGCTCATGAAGTAAAATAA
-+
-HIIJJJJJJJJJCCCFFFFFHHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4193:2190 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCACTTTACAGCTTCTTCTTAT
-+
-IJJJIJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4045:2192 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCACTGTGTTGGCGTTTTATCT
-+
-IJJJJJJJJJJHCCCFFFFFHHHHHIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4171:2195 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGATCGAAGTTGAAGAACCTATAA
-+
-HIJJJJJEHIIJCCCFFFFFHHHHHJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:4159:2232 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCGTATCAAACGTAGAGGCAG
-+
-IIJIJJJJJHHH@@@FFFFFHHHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4186:2233 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTTAGTCAGCTGCAACACTTT
-+
-IJJIJJJIJIJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4072:2235 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTAACACCAAACAACTCTTTCT
-+
-HJJJJJJJIJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4053:2236 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTTGGAGGTTTGAGATATAA
-+
-JJJJIJJJJJJJCCCFFFFFHHHHHJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4001:2239 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTCAAATGAGAACTTTGAAGGC
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4493:2158 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAGNCGTTTGGACGTTGGTAC
-+
-HHIIIIIIIIIH@@#4=DDDHFFHFE=DHACH
- at HWI-ST960:105:D10GVACXX:2:1101:4487:2169 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAAGCATGTAGTTTGATGATC
-+
-IIIGGICFHHII@@@DDDDDHDCABEBEBG>F
- at HWI-ST960:105:D10GVACXX:2:1101:4487:2182 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAAATTGTTACGCAACAAACT
-+
-HFI85DDBCEHH@@<BABADFDDDFGAFGHGC
- at HWI-ST960:105:D10GVACXX:2:1101:4428:2194 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTAAATATTTTTTCTATTCA
-+
-8/=CC68.8=;=@:?BBD;AFBFFFBAGII<A
- at HWI-ST960:105:D10GVACXX:2:1101:4264:2201 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCACTTAATCTGAGTCTCTGCTT
-+
-IIJIJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4422:2216 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCACTTTACACGACAAAATAA
-+
-HGIJIJJJJJJHCCCFFFFFHHHHHJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:4332:2220 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTTCCGAGTACAACTTTGG
-+
-JIIIJJJJIJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4424:2238 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTAATCTTGTGTCGGCAGGTGT
-+
-HIJIHHHFFFFFCCCFFFFFHHHHHJJJJJBGH
- at HWI-ST960:105:D10GVACXX:2:1101:4369:2249 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCGATAATGATGATGAAAGATG
-+
-IJJJIJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4279:2250 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTATGTAGAACTCTTTGCTT
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4589:2160 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTGNTTTGTTTGGTACTGAAA
-+
-IIIIIIIIIIII@@#4=BDDHFHHFHIIIIII
- at HWI-ST960:105:D10GVACXX:2:1101:4565:2165 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCACNTGTGAAAATCTGATTAT
-+
-IIIGHIIIIIII?@#4ADDFFHHHHIIIIIII
- at HWI-ST960:105:D10GVACXX:2:1101:4583:2173 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTAGTGAAATACACTCTCT
-+
-IIIIIIIIIIII??:B?ABBAB?DHGDHG>>@
- at HWI-ST960:105:D10GVACXX:2:1101:4599:2173 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTGTTATCGTGTCTGTAAGC
-+
-JJJJJIJJJJJJ@@@DFFFFDHHBHIIJGJGB
- at HWI-ST960:105:D10GVACXX:2:1101:4699:2181 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTGCCTTCAAGTTAACTTTGT
-+
-GIIHIHIJIJJJ@@BFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4615:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAGTCTTCTTCTTCTGTATTA
-+
-DBGDEHGIGG at C@@@FDDFDDFFHFHBAGDII
- at HWI-ST960:105:D10GVACXX:2:1101:4505:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATCCTATGCTTTGGTCATAT
-+
-IIIGIGGGGIII@@?DDADDH?FHFE<CEHFH
- at HWI-ST960:105:D10GVACXX:2:1101:4515:2195 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTACTTAGACTCATGCTTGT
-+
-HIJJIJJJJJJJCCCFFFFFHHHHHJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:4695:2199 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCAATGACTGTAACTTACTCTTC
-+
-HIJIHIJIJIJJ at CCFDEFFDHHHHIJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4586:2200 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTATAGGAATCTGTAACTTTT
-+
-IJJJJJJJJIIJCCCFFFFFHHHHHIJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4624:2201 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTATTTGCGATGTATCATGTAT
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJHJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4717:2204 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTTTGGTTTATTTACATGTTT
-+
-JJJIJIJJIIJJ at BCFFFDFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4738:2224 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATAGCTTCTCTGTTATGTCT
-+
-HIJJIJJIJJJJCCCFFFFFHHHHHJIJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4745:2243 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTGATATCTAAGCTTATGT
-+
-JJJJJJJJJJJJCBCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4619:2246 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTCAGATTTCTTACATTCAA
-+
-IIJIJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4707:2246 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCAGTGTTTGTCTGAACTCTG
-+
-IGIIJJJJJJJJBCCDFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4784:2161 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTCNGTACTGGTACTGTAATA
-+
-JIJIJJJJIJJJ at C#4ADDFHHFHHJJHEGHJ
- at HWI-ST960:105:D10GVACXX:2:1101:4903:2162 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATNGACAAGTTGGTTTCGAT
-+
-IIJJHIJJJJJJCC#4ADDFHHHHHGIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4957:2163 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTNTGTCCTCCAGACAACCC
-+
-HIJJJJJJJJHHC@#4ADDFHHHHGJGGIJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:4807:2163 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCTNGTTTGTGGTTAGTGTCA
-+
-IIJJJJJJJJJJBC#4ADDFHHHHHJJHIIIJ
- at HWI-ST960:105:D10GVACXX:2:1101:4863:2165 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATNGTTGCGTAAGAATCAGGA
-+
-HJJHHIJIIHHHBC#4=BDDHHHHGIJGIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4754:2182 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATCGTCGTCAAGCCTGCCAC
-+
-HGJIGIJHHHHHCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4768:2182 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAAACTTCTCTGTTTAGTTTGT
-+
-BDFFGDHIDHDF@@?DDDDDHHDDDFCH<?EEH
- at HWI-ST960:105:D10GVACXX:2:1101:4842:2184 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTAATCATTATAGAGATGGT
-+
-HIJIJJJJJJJJCCCFFFFFHHHHGJJJJJJH
- at HWI-ST960:105:D10GVACXX:2:1101:4964:2184 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCAAGTCATGACTCATGAGAT
-+
-JIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4787:2188 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAACAAACTTGCATGTCGGCAC
-+
-IJJJJJJJHHHHCCCFFFFFHHHHHJIJJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4867:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTCTTCTTTCCAATCTTATCAC
-+
-JJJGIIJJIJJJ@@@FFFFFHHHDFGIGGIHII
- at HWI-ST960:105:D10GVACXX:2:1101:4934:2200 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTTGTAGTAACTGAAAACG
-+
-IIJIJJJJJJJJCBCFFFFFHHHHHJJJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4988:2205 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCTTCTTTCTCGAGAAATCGG
-+
-JJJJJJJJJJHHCCCFFFFFHHHHHIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4973:2209 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGCTGTAATTACAGATTGAA
-+
-JJJJJJJJJJJJ@@CDFFFFHHHHGIJIJIGG
- at HWI-ST960:105:D10GVACXX:2:1101:4783:2210 1:N:0: bcd:RPI3 seq:CACTTAGGCATC
-CACTTAGGCATCGATGAATACATCATGGTAGTG
-+
-IJJIJIGHIIJJCCCFFFFFHHHHHJJJGHJII
- at HWI-ST960:105:D10GVACXX:2:1101:4861:2212 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTATGTTTAGTTTAGAAGAA
-+
-FHIIJIJJIIIJ@@@FFFFFHHBHHJIJIIGJ
- at HWI-ST960:105:D10GVACXX:2:1101:4929:2223 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAACTGTGTCTCATCACTCAA
-+
-IIJHJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4966:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATATTCAAACTCTTGGACTGA
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:4877:2249 1:N:0: bcd:RPI2 seq:CACCGATGTATC
-CACCGATGTATCCTTCCTACTTGAAGAAGGTTG
-+
-IJJJIIJJHHHHCCCFFFFFHHHHHJJJJJHIJ
- at HWI-ST960:105:D10GVACXX:2:1101:5072:2160 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGCNTGTCCCTTACTCTGTAT
-+
-JIJJJJJJJJJJCC#4ADFFHHHHHJJIIIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5006:2164 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCTNTCCTCTGAATATTTCTA
-+
-HGIIJJJJJJJICC#4ADDFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5029:2168 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGATCTTTTGGTTCTGTAGACACAC
-+
-IJJJJJJGIJJICCCFFFDFHHGHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5174:2170 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTATATAATATTCCCTAAGAA
-+
-JIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5153:2178 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAATACCCCGAAAATTAGATC
-+
-JJJJJJJJJHHHCCCFFEFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5078:2188 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTCTTGGTCTGGTGGTAACAAT
-+
-HIJJJJJJJJJJCCCFFFDFHHHDHIGHIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5182:2192 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATTTGTCAACTTCAATTTCAG
-+
-HIJIJJJJJIJJCCCFFFFFHHHHHJJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5054:2198 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTACTGTATCTCATTAGCTGA
-+
-HIJIJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5208:2202 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTATGTTTCTCTTGGAACGAA
-+
-HIJIJJJJIJJJCCCFFFFFGHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5105:2206 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCATGAACTGTATTAAACTTTT
-+
-JJJIIJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5029:2212 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAACATTTCGAACAATGAACAA
-+
-HIJJJIJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5084:2222 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTACCTCTCTCTGACTTCAC
-+
-IJJIIJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5223:2223 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCCGGAGTTTTTTCAGCAGTTC
-+
-JJJJJJJHHHHHBCCFFDDFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5173:2228 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTATGTGTAATGATTCCTTC
-+
-JIJJJJJJJJJJBB at FFEFEHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5208:2240 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATTTACTTTGATCAGAAATT
-+
-JJIFHIIGHIJJ at BCFFFFFHHGHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5101:2247 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAAACTCTACCTTTATTACAGT
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5189:2247 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCTACAAAACTTTCTAATTTG
-+
-IHJIJJJJIJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5018:2248 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTATGTAGAATATGAGTTTA
-+
-IJJJJJJJJJJJBBCFFDFFHHHHHJJJHIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5160:2249 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTGCTTGATTTTGAAGTTAG
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHIJJHIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5491:2158 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTCNCTAAGATTCGACCCTCCC
-+
-HIJJJJJHHHHHCC#4ADDFGHHHGIJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5363:2158 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTNTGATTGTAGTCAGAACC
-+
-IIJJJJJJJJJJCB#4ADDFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5471:2159 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGNGGGTTTGGCTTGAAACTC
-+
-HIIIIIIIIGIH@@#4=DADDFHFHIIGGII at E
- at HWI-ST960:105:D10GVACXX:2:1101:5293:2163 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATNATAGACCAAAAGCAATTC
-+
-IJIJJJJJJJIJCC#4ADDFHGHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5262:2165 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTCNAACTTTGAGGCTTAAAAA
-+
-HJH<DDE@@AC=CC#4ADDFHGHHHJJJJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5313:2166 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTNTCATATTTGCGATGTAT
-+
-JJJJJJJJJJJHCC#4ADDFHHHHHJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:5498:2182 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAGCGAGAGTTCTTGAACTGA
-+
-IJJJJJJIJJJJBC at FFFFFHFHFHGIIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5435:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTATAAGGACTGTGAAGTGTG
-+
-JIIJIJJJJJJJCCCFFFFFHHHHHJJJGHJI
- at HWI-ST960:105:D10GVACXX:2:1101:5472:2190 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCACTGTAATCTCACGGTGTGT
-+
-IIJJJJJIJJHHCCCFFFFFHHHHHJJJHHGIJ
- at HWI-ST960:105:D10GVACXX:2:1101:5358:2205 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTATGTAATGTAGTCTTTAAA
-+
-IIJJJJJJJJJJCCCFFFFFHHHHHJJJIIHJ
- at HWI-ST960:105:D10GVACXX:2:1101:5420:2213 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCGTTTGATTTGCAAGCTG
-+
-HEIJIIJJJJJJCC at FFFFFHHHHHJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5318:2214 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATTTGTAGCAAGGCACTGAT
-+
-IIJJJJJJJJJJCCCFFFFFHHHGHIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5357:2223 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCTTCATTTCTGCTCTTATCAC
-+
-BBF at FCGHDFGH@@CDDFFFFHDDHIIIG at EIG
- at HWI-ST960:105:D10GVACXX:2:1101:5300:2224 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAATGTAGAACACACATGATTT
-+
-FBF=CFEFGEEE?@@?DDD;:DBFFFFIF+AIF
- at HWI-ST960:105:D10GVACXX:2:1101:5485:2228 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAAAATATCGTATCCGTTCAA
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5295:2241 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCAAAGACTTGGACCTTCTTTC
-+
-B=FHFBDF===C@?@DBDDBFBFHHGGIIGGIB
- at HWI-ST960:105:D10GVACXX:2:1101:5281:2244 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGGAGCGTACCGACATGCGGT
-+
-EFFDFFDEEEEECCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5593:2158 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAANCTTAGAGTCTGTTTTTT
-+
-HGIFHHHHHEEE@@#4=BDDHH?FHHFHIIEI
- at HWI-ST960:105:D10GVACXX:2:1101:5636:2160 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCTNCGATGATGATCAAATCAT
-+
-IIJGJJJJJIGICC#4ADFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5558:2161 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTNCTTGGGTTCAACTGCCTT
-+
-=BCFFCFF at EEE?:#4=BDDFCFFFFCED at EBH
- at HWI-ST960:105:D10GVACXX:2:1101:5611:2162 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTNAGAACTTGATCATGCAT
-+
-IIJJJJJJJJJJC@#4ADDFHHGHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5679:2172 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTAACAATATTCTCATGCACCT
-+
-HJJJJJJJJJJJCCCFFFFFHHGHHJIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5663:2184 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTTTGTAATCTGACTCTCTT
-+
-IGIG?HIJHIJJC at CFFFFFHGHHHJJJIJII
- at HWI-ST960:105:D10GVACXX:2:1101:5539:2195 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTGAAAGAAAGAGCCATTGGT
-+
-HIJJJJJJJJJJCCCFFFFFHHHHHJJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5728:2197 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATCTGTATAAATAGTTTTAA
-+
-HHJJJJJJJJJJCCCFFFFFHHHHHJHIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5500:2203 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTATCAATTGAACTAGATTCA
-+
-IJJIJJJJJJJJCCCFFFFFHHHHHJJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5592:2204 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGATCAATAAAGCTGTTGAATGAGAT
-+
-HJJJJJJFHIJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5553:2233 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCGATCTGTAAACTAAAAAAAC
-+
-IJJIJJHHFFFFCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5604:2241 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATTTGATTACCATAGCATTT
-+
-JJJJJJJJJJJJCCCFFFFFHGHFDIHIJIIJ
- at HWI-ST960:105:D10GVACXX:2:1101:5743:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAAGGTTTTAAGTTCTTAGAAC
-+
-IJJHJIJJIJJJCCCFDEFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5682:2243 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTCTTGAGTATGTAGAATCTG
-+
-IIJJJJJJJJJJCCCFFFFDHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5999:2166 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTCNCTCTCTCTTTAGTTGTT
-+
-JJJEIJJJJJJJCC#4ADDFHHHHHJJIJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5979:2179 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCTCTCTAGAAAATATCAGA
-+
-HIJIIJJJJIJJCCCFFFFFHHHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5958:2186 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGCGATGATGATAAAATAGC
-+
-IIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:5985:2215 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTATAGTTTTGTTGTTTCTT
-+
-IGIIIIJJJJJJCBCFFFFFHHHHHJHJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5952:2229 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTAGCAGTACAATTGCAGAAGT
-+
-HJJJJJJJJJJJCCCFFFFFHHHHHJJJJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5970:2231 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCTTATGTAGTCTCATTTCCT
-+
-HBGDHGHIIGGI at CCFFFFFHDFHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5909:2233 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCACCAGTTTTACAGAGTGTTT
-+
-JIJJJJJJJJJJCCCFFFFFHHHHHJJEHHJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5792:2239 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTATATACTTCACAACTCTG
-+
-JJJJJJJJJJJJCBBFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:5990:2248 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCACGGGAAGGTGATATTTGCT
-+
-JJJJJJJJJJJJ at CCFFFFFHCFHGJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6177:2163 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTANCATCGCTTCGTTTTTAT
-+
-HHJJJJIJJJHHC@#4ADFFHHHHHHIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6014:2179 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTACTTCTAAGTTTAGTAAC
-+
-JJJJJJJJJJJJCBBFFFFFHHHHHJJJIIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6138:2192 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCTTTATATGAACCAATAATAG
-+
-FGHIGGHIIJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6181:2194 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATCACAAAATATATAGGAAGT
-+
-IIJJJJJJJJJJCCCFFFFFHHHHHJJJJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6001:2199 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTTGTGAATCTGATTATACAC
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6161:2202 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTAAGTCATAATAATAGTAGC
-+
-GHIJJJIJJJJJ at BCFFDEFHHHHHJJJJHHIJ
- at HWI-ST960:105:D10GVACXX:2:1101:6053:2206 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTTTGTTGGCATGAGAACCAA
-+
-HIJJJJJJJJJJCCCFFFFFHHHHHJJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6128:2212 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCATTGTTGTACTCTTTAATAT
-+
-GIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6082:2221 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATTTTGTGTGAAAAAAAAAA
-+
-B;CECAEDDDDD at CCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6229:2231 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTTTGGTGAAGTTTTTAAGT
-+
-JJJJJJJJJJJJCCCFFFDFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6024:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTAAACCTATAATATTTCTT
-+
-IJJJJJJJJJJJCBCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6181:2236 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTCGGCTAATACCTAATGTCA
-+
-IGIIIJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6060:2238 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTGAATCATGTTGCTTTACT
-+
-HHIJJIJJJJJJ at B@DFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6084:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAATGTGTTCTCTCTGTTCAA
-+
-IGIJIJJJJJII at CCFDFFFHHHHHJJHGIIJ
- at HWI-ST960:105:D10GVACXX:2:1101:6273:2161 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTNACTGTCTTTGGACCCTTT
-+
-GGIBHFCHGGFF=@#4=BDDFHGHHJIGIJIIJ
- at HWI-ST960:105:D10GVACXX:2:1101:6431:2161 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTANTGGTGATTTGTCTGTAT
-+
-IJJJIIJJJIIJCC#4ADDDHHHHHGHJIHIJ
- at HWI-ST960:105:D10GVACXX:2:1101:6304:2163 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATNTGATGTTATAGTAAGCAT
-+
-JJJJJJJJJJJJCC#4ADFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6492:2184 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCTTCACATTATGAATATCAA
-+
-JJJIJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6252:2185 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTATATACTTCACAACTCTG
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6273:2186 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAATGTTGTCTCTCCCTCTTAT
-+
-IJJIJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6457:2201 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTGTGAAACTCTATCAATTCA
-+
-JIIJIJJJJJJJBC at DFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6377:2203 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGAATATGTTGCTGTAGTCAC
-+
-IHJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6427:2203 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCAAACCAGAGACAAATGACAC
-+
-JIJJJJJJJJHHCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6279:2218 1:N:0: bcd:RPI2 seq:CACCGATGTATC
-CACCGATGTATCTTGGACTGTGAAGTTTGGCT
-+
-JIJHGGGICGHHCCCFFFFFHHGHHGGIJJII
- at HWI-ST960:105:D10GVACXX:2:1101:6366:2222 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAGATGTCGGCGTTGAATAAA
-+
-IJJHHHHHHFFFCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6393:2231 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTATTGCAGTAGAACATAAGT
-+
-IHIJJJJJJJIICCCFFFFFHFFHHJJIIJIF
- at HWI-ST960:105:D10GVACXX:2:1101:6268:2234 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAACTCTTGTGTACCATAAAAA
-+
-IIHIIJJJJJJJCCCFFFFFHGHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6467:2241 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTATCACCATGTTCCAATTTC
-+
-IGIIJJJJJJJJCCCFFFFFHHHHHIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6481:2244 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAATACTAGTGTTTAAGAAGTT
-+
-IJJJIJJJJIJJ at CCFFFEFHHHHHJJJGIJJI
- at HWI-ST960:105:D10GVACXX:2:1101:6397:2246 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTAACTTTGGCGAATGGATAC
-+
-@@FFGGII;AHC@??BDDADHBFDF?CFEGIGI
- at HWI-ST960:105:D10GVACXX:2:1101:6429:2247 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTATATATGGAGAAAATGGA
-+
-IIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6523:2161 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATNAGTACTATGTTCTCATTT
-+
-FCFIGIIIIGEF@@#4=2ADFBDAFFFIIBHII
- at HWI-ST960:105:D10GVACXX:2:1101:6687:2163 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCTNGTAGACTCTGTTTTGTC
-+
-IIJJJJJJJJJJCC#4ADFFHHHHHJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:6525:2176 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCACTGTAAGCTGAGGAACTCT
-+
-IGIJJIJJIJGICCCFFFFFHGHHHJGIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6517:2192 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTATGGCACGGCTATGAAATCT
-+
-IHGBEIGHCHHH at CCFFDFDDFHHGIEIIIGGH
- at HWI-ST960:105:D10GVACXX:2:1101:6700:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCACATCTCACTGCTCACTACTC
-+
-HJJGJJJJGIJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6538:2194 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTGCTAGAGAGAGGAGGAGAC
-+
-JJJJJJJJJJHHCCCFFFFFHHHHHJJJJIIJ
- at HWI-ST960:105:D10GVACXX:2:1101:6575:2195 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGTTTTAACACCTCTACTTTT
-+
-HIIHIJIJJJJJBB?DFFFFFGHHHJJJHBHJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6501:2202 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCTTTATGGCTCTAGTACAAGC
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJGIIIJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:6631:2202 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTATCTCTAAAATTGCAAAT
-+
-JJJJJJJJJJJJCC at FFFFFGHHHHJJIIIII
- at HWI-ST960:105:D10GVACXX:2:1101:6672:2205 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGATCATGGTTGCTTTAATATTTTT
-+
-JJJJJJJHIJHHBCCFFFFFHHHHHJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6579:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCGACTTTGATCCAAAAAAAA
-+
-HAHEHHGFFFFFC at BFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6552:2217 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCATCTTTAGCTTTATTTACTC
-+
-IJJJGIJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6685:2223 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCATTATTATCAATAGCTCTTC
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6503:2223 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTTAGGGGCTGATTTGTCTT
-+
-JJJJJJJJJJHHCCCFFFFFHHHHHJJJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6613:2224 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTCTACCATTATGCACTATTT
-+
-IJJJJJJJJJIJCCCFFFFFHHHGHJJJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6670:2231 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCGGCGTGAAAGGGCGACTAAA
-+
-HHHHFFFFEEEECCCFFFFFHHHFGEIGIGIJH
- at HWI-ST960:105:D10GVACXX:2:1101:6721:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTAAACTTTCTTAGCTTGTCC
-+
-IJJGIIJJHIJICBBFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6642:2234 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGGGTGATGAACGAAATAAAAA
-+
-IIJJJJJJJJJJBCCBDFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6589:2242 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATTAAAGACAGAGAGATAGA
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6684:2245 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGATCGAAACCAAACACCGAT
-+
-IGJHHHHFFFDECCCFFFFFHHHHHJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6942:2160 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAANGGTCGATTTAGTTAAAA
-+
-HGIIJIJJJJFI@@#4A=BDHHHHHJGGIIIJ
- at HWI-ST960:105:D10GVACXX:2:1101:6987:2160 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTANACCAGCTGAAGAAAAGGC
-+
-HIJIIJJJIAEHCC#4ADDFHHHHHJJJJJJIF
- at HWI-ST960:105:D10GVACXX:2:1101:6968:2161 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCATNTTGATCGGATGGGCAGAA
-+
-GIIHGGIJHHHHBC#4ADDFHHHHHJIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6922:2166 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTNTGGAACTGTGGATTAAAA
-+
-IJIIJIJJJJJJCC#4ADDFHHGHHIIJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:6902:2167 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTCNTCTTATTCTTTCTCTTT
-+
-IIJJJJJJJJJJCC#4ADFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6830:2173 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCTTGTCATTCTCTAAATAAC
-+
-IIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6954:2174 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTATAACTCTCTCGCCTTTGT
-+
-IJJIJJJJJJJJCBCFFFFFHHHHHJJJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:6754:2179 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTAAGTCGTATCTAGGTGTGT
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJGHIHJ
- at HWI-ST960:105:D10GVACXX:2:1101:6877:2188 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAACAAAGTCGTTGTAGTATAC
-+
-JJJIJJJJIJJJCCCFFFFDHHHHHJJJIHJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:6970:2193 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATCACACTGTCAAATCCGAA
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6918:2197 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATTCGGCTCTGTTCATATAC
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6851:2211 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTTTCTGGCTGTAGAATCTT
-+
-IIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6836:2224 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCACGCACACCGCGTGTAGAG
-+
-IHHHHHHFFFFFCCCFFFFFHHHHHHJHJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6948:2228 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCCGATAGAGAACCTTGCTGACC
-+
-HIJJJJJJJIJJCCCFFFFFGHHHHJIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6923:2230 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTATTTTATGTGGTGTTACTT
-+
-IJJJJJJJJJJJ at BCFFFFFHHHHHFHIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6971:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATCAGTGATGAAATTATGTC
-+
-HIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6883:2236 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGAGTGAGATATAAAATGGG
-+
-IJJJJJJJJJJJCCCFDFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:6822:2246 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGAATTCAGACTGTGAAACTGC
-+
-IDHIIEG:FHIH??;AD?DAFBAFCEHHIEGGC
- at HWI-ST960:105:D10GVACXX:2:1101:7194:2161 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCTNCTTTATATGAACCAATAA
-+
-C8B88FF:C3=@@@#4=AD;FBFFDBFBBF?FA
- at HWI-ST960:105:D10GVACXX:2:1101:7080:2163 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTCNGGATTCTCACTCTCAGC
-+
-HHJJJJJJJJJJCC#4ADDFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7018:2176 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGATCGGAGTTTTTTCAGCAGTTCT
-+
-JIJJIIJDHIJJBCBFDEFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7182:2176 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATTGTATTTGTGCGTGTAGC
-+
-JIJJJJJJJJJJBCCFFFFFHHFHGJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7145:2178 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATAATAAGACTCTTAATCAA
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7091:2178 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTATGTAATGTAGTCTTAAAA
-+
-JJJJJJJJJJJJBC at FDEFFHHGHFHIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7123:2181 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTCCTTGACTGGAAAAATGT
-+
-JGIJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7068:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTAATGTACCGATGCATAGT
-+
-HHJJJIJJJJJJCBCFFFFFHHHGHJJHIIEH
- at HWI-ST960:105:D10GVACXX:2:1101:7245:2192 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGTTTACCATGGAACGAACAT
-+
-HJJJJJJJJJJHCCBFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7109:2196 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATTGTAATTCAGTTAGCTCAA
-+
-IIIJJJJJJJJJCCCFFFFFHHHHHIJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7209:2197 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTTGTCAATGCATAGACAAAA
-+
-JJJJJJJJIJJJCCCFFFFFHHHHHJJJJJJJG
- at HWI-ST960:105:D10GVACXX:2:1101:7060:2201 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTGTGTGTTGGTGGATATAAC
-+
-IGJJJJJJJJJJBBCDDEFFHHHFHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7155:2215 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTTGTTGGCCTTTAAAAAAA
-+
-HDGBGHHFFFDDC at CFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7198:2217 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTATATATTTCGTTTCATTT
-+
-HGIJGHIJJJJJCBCFFFFFHHHHHJJJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7115:2229 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTAAGGCTGTGGAGGTTATC
-+
-HIIIIIIIIIIICCCFFBDFHHHGDGGHHHAH
- at HWI-ST960:105:D10GVACXX:2:1101:7149:2234 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTTTGTTAGACTCTTCGATTT
-+
-IJJJIJJJJJJJCBCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7127:2244 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTATGTAGATACTGATATTA
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7018:2247 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCTTTATATGAACCAATAATAG
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7448:2162 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCAGNGTGGATGCTGCGGAAGAT
-+
-GGIJIJHHHHFFBB#4=DDFHHHHHJJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7352:2162 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTNTGTTGTGGGTGACTTTGA
-+
-IJJJJJJJJJHHCC#4ADFFHHFHDGHJJJIJI
- at HWI-ST960:105:D10GVACXX:2:1101:7420:2163 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCACNGTGTTGGCGTTTTATCT
-+
-IJJJJJJJJHHH at C#4=DDFHHGHHIJJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7296:2163 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTCNATCTGTCGTACTGTTGT
-+
-IJJJJJJJJJJHCC#4ADFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7382:2185 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTAGTAGACTTGCAAAGATCGT
-+
-HIJJJJJJJJJJB@@DDFFDDHHGHJIIJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7449:2187 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAATACCCCGAAAATTAGATC
-+
-IGIJJJJJJHHHBCBFFFFFHHHHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7359:2193 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAGGCTGATTGTAGAATGGTT
-+
-HGHJJJJEGIII@@@FF>DFHFFFFGIIJJII
- at HWI-ST960:105:D10GVACXX:2:1101:7292:2202 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTCAATCCATGGTTTTCTCAAAGTTTTC
-+
-HJJJJJJJJJJJCCCFFDFFHHHHHJJJHIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7393:2205 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTATGTCTCTGTACTGTAAC
-+
-JIJIJJJJJJJJC at BFFFFFHHHHHJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7359:2210 1:N:0: bcd:RPI1 seq:CACATCACGATC
-CACATCACGATCAGAGATCGGAAGAGATGGCTT
-+
-JFGGHHJJGEHH at C@FFFFFHGHAFGIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7415:2224 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATTAATTATTCGTATGAACT
-+
-IIJIJJJJJJJJ@@CFFFFFHHFHHJJIIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7403:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCGTCTTACCATTTCTTTCAT
-+
-III@=F4./@FI@@@A?DD>AC>BF at GFGBHI
- at HWI-ST960:105:D10GVACXX:2:1101:7373:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTATGTCTGTCTAGTCTATTG
-+
-IHIGIJIJJJIJ at CCFFFFFHHHHGHIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7324:2231 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAATCAAATGTATTATATATAT
-+
-IJJJJJJJJJJJC at CFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7309:2246 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTGAGTTTTTACATGTTTGT
-+
-IIJJJJJJJJJJ at BBFFDFFHHHHHJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7475:2247 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTTGACTGTATTGAGCAACC
-+
-IIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7687:2161 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTNTAGTCTAAGGCTTTTCAA
-+
-HIJJJJJJJJJJCC#4BDDFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7649:2170 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCTGAGTAGACAATTTAATCA
-+
-F?B at FHGIJGEH@@@FADEFHHHFHJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:7708:2170 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAGTTTAATAAAACAGAACAA
-+
-IJJJJJJJJJJJCCBDFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7709:2191 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTCTCTCTCTTACCTTTCTCT
-+
-JJJJIJJIJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7690:2197 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATTCGATTAGTACCGTTAGTG
-+
-IIIEIHIJJIHHCCCFFFFFHGHHHJIHIIJIG
- at HWI-ST960:105:D10GVACXX:2:1101:7607:2203 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCCGGAATGGTGCCTTTGTTAC
-+
-HJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7698:2214 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCTCTGGCTTTGCTCAGATTT
-+
-IJJJJJJJJJJJ at BCFFFFFHHHHHJJJIIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7518:2217 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCAATTCTTTTACCGGGTTGAG
-+
-HHIJHJJJJHHHCCCFFFFFHHHHHJJGHJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7534:2218 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATAATGAATGTTTCGGACTTC
-+
-FFGIJIEHIJGH at CCFFFFFHHHHHJJIGIIJG
- at HWI-ST960:105:D10GVACXX:2:1101:7679:2220 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATCGGTGAGTGGAACTTCTT
-+
-IJJJJJJJJJJJBCCFFDDDHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7747:2228 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCACGAGTCGAGGCTCTCAATA
-+
-HJJJJJHHHHHHBCCFFFDFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7610:2232 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTCAGTGGTAGAGCGCGTGGC
-+
-HHHHHFFFFFFECCCFDFFEHHHHHJJJHIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7532:2235 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTATGTTCACTGTTCTCTGC
-+
-DBFFCCFHGGEG?@CFDDDDHHHHHGGJJGIJ
- at HWI-ST960:105:D10GVACXX:2:1101:7676:2238 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGATCCAGCCGTCGGATACTGACTT
-+
-IIIIIHHACHHF<@@FFFFDHHHHHDDHIIII
- at HWI-ST960:105:D10GVACXX:2:1101:7641:2240 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATCTGTAGCCTCTCTTTTAGT
-+
-HIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJH
- at HWI-ST960:105:D10GVACXX:2:1101:7824:2158 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTNAGTCTCTTTTTTGAATT
-+
-GGHDHHIEGHGH@@#4=ADBFHHHGIIGIGGI
- at HWI-ST960:105:D10GVACXX:2:1101:7876:2164 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAANACATGGGAAAATATGTG
-+
-==='566A@===@@#442AAAD?CB?C at G>IB
- at HWI-ST960:105:D10GVACXX:2:1101:7774:2165 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCTCNAACGAGGAAAGGCTTAC
-+
-JJJJJJJHHHHFCC#4ADFFHHHHHIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7839:2165 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTNTAAAACTGTGCCATTAT
-+
-IJJJJJJJJJJJCC#4ADFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7920:2167 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAANTTCTTTATACTTTGTAAA
-+
-HIJJJJJJJJJJCC#4ADFFHHHHHJJJJHIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7966:2176 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATGCAACTGCAAATTCTGCA
-+
-JJIJJJJJJJJJCCCFFFFFHHHHHJJJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7948:2186 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTTGCTGTGGATGATCTGGT
-+
-HIJJIJJJJJJJ at CCFFFFFHHGHHJJJJJJH
- at HWI-ST960:105:D10GVACXX:2:1101:7864:2190 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCGGAAGAACTCTGGAAGTGAA
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJHIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7912:2193 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAACAAGATGTTTAATCATCC
-+
-HIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7970:2195 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCACAATTGTTGTCTTGTAGTA
-+
-IIJGHJJJIIGJ at C@FDFFFHHFFAHIHIJHH
- at HWI-ST960:105:D10GVACXX:2:1101:7819:2202 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTAATTGTTTCTTAGCATCT
-+
-IJJJJJJJJJJJCBCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7762:2204 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTACTTTATAAGGACTGTGAA
-+
-IJJIJIJJJJJJCCCFFFFFGHHHHJJJIIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7847:2207 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATGCAACCCTGTCTTGCTTTA
-+
-IJJIIJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7775:2219 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTATTGTGTTACTGAATCTT
-+
-JJJJJJJIJJJJCCCFFFFFHHHHHJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7900:2219 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATTACGCCCGAACGCAAACC
-+
-HFFFFDDDEDDDCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7800:2227 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCTCTTATGATGTCAAAACTTTC
-+
-HIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7973:2227 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTATGTGTTCTGCAGATCGA
-+
-IIJIJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7844:2229 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTTCGTTGGGTTTTCTTCAT
-+
-IIJJJJJJJJJJ at BBFFFFFHHDHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7863:2232 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATAAATTTTCGAAGGAGACAA
-+
-HIJJJIJJIJIH?BBFFFFFHHHHHJIJJIGII
- at HWI-ST960:105:D10GVACXX:2:1101:7912:2234 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCGTGTGTAACCTCATATGGAC
-+
-IIJJGIJJJJJJCCCDFFFFHHHHHJJJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:7940:2245 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCGTGTCAAGTGTAGAATCAA
-+
-IJJJJJJJJJJJBBBDDFFFHFHHHIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8088:2158 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCANTGGAAGGCTGTGGAGGA
-+
-IJJJJJJJJJHHCC#4ADFFHHHHHHIIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8140:2163 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCCGNTGGGTTGGGGATCCGGT
-+
-HEHE at DBDBCCC@@#4ADB=?DDDHIAFBE@?
- at HWI-ST960:105:D10GVACXX:2:1101:8156:2163 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATNTGTAAGTATGAACAAAA
-+
-IIIIJJJJJJJJCC#4ADFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8057:2166 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAGNAACATTGAACAAGCAGTT
-+
-IJJJJJJJJJJJCC#4ADDFHHHHHJJJJIJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:8023:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATGTATCTTGTTGTTTATCTA
-+
-HIJJJJJJJJJJCCCDFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8157:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTCAGTGGTAGAGCGCGTGGC
-+
-EHHFHHFFFFFF at BBFDFFDFHGHHJIJIIJI
- at HWI-ST960:105:D10GVACXX:2:1101:8117:2186 1:N:0: bcd:RPI3 seq:CACTTAGGCATC
-CACTTAGGCATCACTGAATCGACTTTGGGCAAA
-+
-HJJIIHFHIJJJCCCFFFFFHHHHGGIJJIIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8197:2187 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATGGTGCTTAAAAAAAAAAA
-+
-C;@>BBDDACCA at CCFDEFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8236:2188 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTATGTCGGCTTAAACTCTAT
-+
-FGIIJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8088:2193 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTATGGAAATGTGCTATGGAC
-+
-JJJJJJJJJJJJCCCFFFFFHHFHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8085:2226 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTCGCAGTCGCTAAGCGTCAC
-+
-JJJJJHHHHHHFCCCFFFFFHHHHHJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8003:2228 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATATTTGTGGATGATGAAGA
-+
-IIJJJJJJJJJJCCCFFFFDHHHHHJJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:8138:2242 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTATATGATTCTACTTAGTCA
-+
-IJJJJJJJEIJICCCFFFFFHHHHHJJJJJIIJ
- at HWI-ST960:105:D10GVACXX:2:1101:8069:2250 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGGTACTATGAACATTGTGAC
-+
-HGIIGGIGHIII at CCDDFFFHHGHHJJJIIIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8445:2158 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTNAGATTAGACTCTGTTTGC
-+
-IJJJJJJJJJJJCC#4ADFFHHHHHJJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8271:2161 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCTNTGTATAATTGGAACAAG
-+
-HIJHGIJIHIGIBC#4=ADFHHHHHJIJIJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:8390:2167 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTNCGTGTAGAAGGGAAATGA
-+
-IJJJJJJJIJHHCB#4ADDFHHHHHJJJJJIII
- at HWI-ST960:105:D10GVACXX:2:1101:8355:2173 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTATGTGTAACCCTGTCCTT
-+
-IJJJJJJJJJJJCCCFFFFEHHHHHIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8375:2177 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATATTGCTATAGAGTCACGCATCT
-+
-IJJJJJJJIJJH at CCFFFFFHGGFHIIIGIJII
- at HWI-ST960:105:D10GVACXX:2:1101:8257:2177 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCACCTGGAGACTCATGTGTTGA
-+
-IJJJJJJJIJJIBCCFFFFFHHHHHJJIJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:8438:2178 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTTGGTTTGGATTTTGGTTA
-+
-IJJJJJJJJJJJCCCFFDFFHHHHHJJJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8299:2178 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATCTCTGGCTGTTGAATAGA
-+
-IJJJJIIJJJJJCCCFFFFFHHHHHJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8333:2183 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAGCTTGCAAGTTCTCTCTGAA
-+
-HJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8309:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCACTGTGTTGGCGTTTTATCTG
-+
-IJJJJJIHFHHH at CCFDFFFHHGHHJIIJIJJI
- at HWI-ST960:105:D10GVACXX:2:1101:8363:2198 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCAAGCATGATGAATTGATGAG
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8494:2200 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTTTGCATTGATTGTGGTTAC
-+
-HIJJJJJJJJJJCCCFFFFFHHGHHJIJIGGJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8291:2212 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGATCTCTACTCTACTAAACCTCTGT
-+
-IJJJJJJHIJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8482:2215 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATCTTCCGTCTGTTTCTGAT
-+
-HGIHIIJIHHGICCCFFFFFHHHHHJJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:8322:2218 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCTTGACCGATGCTCGGACAA
-+
-HGHHHHHFFFFECCCFFFFFHHHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8388:2225 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGATCGTGTGTATTTAGTAATTCAT
-+
-JJJJJJJGIJIJ at B@DDEFFHHHHHIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8442:2226 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATTTTCTATGTTGTTTGGTAG
-+
-HIJJJJJJJJJJCCCFFFFFHHHHHIJJJJFII
- at HWI-ST960:105:D10GVACXX:2:1101:8339:2233 1:N:0: bcd:RPI2 seq:CACCGATGTATC
-CACCGATGTATCATCTCTAGAACTCTTTATAAT
-+
-HIJJIJJJHIJJCC at FFFFFHHHHHJJJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:8376:2238 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATGTGTCAGATTCTAAAAAA
-+
-IIIIIHHIIIII@@CDFFDFHFDHHBHGIIII
- at HWI-ST960:105:D10GVACXX:2:1101:8457:2246 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCACTCTGTGGATTATGCTTTA
-+
-IGIJIJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8675:2161 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTNTAGTAGAATTGGTTGCAT
-+
-IGIIIIIIIIII@@#4ADDDHHHHHIIGIIIII
- at HWI-ST960:105:D10GVACXX:2:1101:8657:2165 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCGANCGTTTCTCTAGTTTTGT
-+
-IIJJGJJJJJJJCC#4ABDDHHHHHJHIJJJG
- at HWI-ST960:105:D10GVACXX:2:1101:8627:2171 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAGGTAAATTTGTCTGAATTA
-+
-JIJJJJJJJJJJBCCBDFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8743:2178 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATCATCTTTTCTTATGTAAA
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJIHHJG
- at HWI-ST960:105:D10GVACXX:2:1101:8722:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTATGTAGAGAAAGTGATTA
-+
-IIJJJJIIJJIJCBBFFFFFHHHHGJ<EHIEG
- at HWI-ST960:105:D10GVACXX:2:1101:8678:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTGATGTATATTTACGAGATGT
-+
-HJJJJJJJJJJJBC at FFDFFHHHHHJJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8565:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTGTCCTTCGGATCACTCAATT
-+
-HJJIIJJJIHHHCC at FFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8583:2192 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTAACGCTTTTATGTGCTTCT
-+
-HIIIIJJJJJJJCB at FFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8633:2194 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTATACATATTGGGTTGTGATT
-+
-HJJJJJJJJJJJCCCFFFFFHHHHHHIJHHIIJ
- at HWI-ST960:105:D10GVACXX:2:1101:8687:2198 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATTTCTGTAGACTATGTGTTG
-+
-JJJJJJJJJJIJ at B@FFFFFHHGHFIIGHHJEG
- at HWI-ST960:105:D10GVACXX:2:1101:8605:2201 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGATCTTTCTTGTCTAGTCGGTTTAT
-+
-IIJIJJJEHIJICCCFFFFFHHHHHIJJHIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8532:2207 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAATGAATGTGTAGAAAAAAA
-+
-HIJIJJHHHHHFBCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8688:2216 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTGGGGAAGGATCAGATGCA
-+
-HGIIJJJJJJIJ at BBFFFFFHHHHHIIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8560:2228 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAATTGGTGCCTGTAGGTCAG
-+
-HIJJJJJJHHHH at CCFFFFFGHHGHJJJIIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8658:2230 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCTGCTATAGAATCTGGACAAA
-+
-IIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8538:2232 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTCTTATCTTTTACTTTCCTC
-+
-IJJJIJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8669:2248 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTACTGTTTTTTCCGCCTTC
-+
-HIJIJJHHHHFFCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8931:2159 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATNGCAGTCTCTGTAGAATAA
-+
-JIJJJJJJJJJJCC#4ADDFHHHHHIIIJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8978:2160 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTNAGTGGATATATTCATTAC
-+
-IIJJJJJJJJIJCC#4ABDFHHHHHJJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:8804:2166 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGNAGAAGTGTTAGATATAGT
-+
-HJJJJJJJJJJJBC#4ADDFFHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8917:2174 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATGTTGTTGTTGCATGCTGTG
-+
-JJJIJJJJJJJJBCCDFFFFHHHHHJJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:8755:2195 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATGATGTCGTTGGGTCTTTGT
-+
-B==/;6.;==A?@@@DDAD?FHF??FEEED at AH
- at HWI-ST960:105:D10GVACXX:2:1101:8885:2196 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCTCCGATGATGATCAAATCAT
-+
-IIH:F;@FDHII@@@DABDDHDBFHAEHFHAE
- at HWI-ST960:105:D10GVACXX:2:1101:8967:2201 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTTCTTTATTCCTGGGTTGT
-+
-IJJJIJJJJIJJCCCFFFFFHHHHHJJJJGHIJ
- at HWI-ST960:105:D10GVACXX:2:1101:8797:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTTAACTCTTGCCTCTTCTT
-+
-JIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8831:2214 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTTTGGGTTTGTGGTGGGGGT
-+
-EEDDDDDDDDDDBCCFFFFDHHHHHJEGIJJJF
- at HWI-ST960:105:D10GVACXX:2:1101:8957:2220 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGTCTTTAGCATCGACTGTT
-+
-IJJJJJJJJJJJCCBFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8751:2221 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGTGTTTGTGTTTAAGTGCT
-+
-HIJJJJJJJJJJBCBDDFFFHHHHHJJJHIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8914:2223 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCGTTTTGGCTTTCGTTCTGT
-+
-JJJJJJJJJJHHCCBFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8937:2229 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGATCTGGAATGATGATAACGATTTT
-+
-JJJJJJJHHGIJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8832:2238 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTTGTCAGTCTAAGAAAATG
-+
-IJJJJJIJJJJJBCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8894:2244 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCGAATGTTTAAATTGGATCAA
-+
-IGIJJJJJJJJJCBCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:8849:2246 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTTACTGTAGTATATATGAT
-+
-JGIJIJJJJGHJBCCFFFFFHHHHHJJJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9183:2160 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTANAACCTGTTGAATTTATA
-+
-IIJJJJJJJJIJCC#4ADFFHDHHGIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9200:2160 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCACNTAGCGAAATGCGATACTT
-+
-HIIIIGHEAEA@@@#4=DDDAFFHHDHIIIIII
- at HWI-ST960:105:D10GVACXX:2:1101:9117:2160 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCANTTTAGTTTGGTACTAAT
-+
-HIJJJJJJJJJJBC#4ADDFFHHHHGIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9238:2160 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCTANATTATACAATGTCTCTGT
-+
-IJJJIIJJJGIJCC#4ADFFHHHHHJHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9130:2168 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAGGAATTGTTGAGTTTGGTA
-+
-IIIB=B;@=@FI;?@BADDDFF?ADEFFEF<A
- at HWI-ST960:105:D10GVACXX:2:1101:9203:2174 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCTTGACTGTGATTTAAACGAG
-+
-==FB at FDDF@@E??@DDEDDDHAHHGGIIEEF
- at HWI-ST960:105:D10GVACXX:2:1101:9183:2182 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTACTCTATCTTAAACATGT
-+
-HIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:9125:2192 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTATCGGATTGTCAAATGTCT
-+
-FHHIIGHIJJGICCCFFFFFHHHHHJJJICJH
- at HWI-ST960:105:D10GVACXX:2:1101:9001:2202 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCTTCTTGTTGTCTAACTCTC
-+
-IGI67B at A7CEH@@@DDBDDD?CDDGHBFAFE
- at HWI-ST960:105:D10GVACXX:2:1101:9175:2204 1:N:0: bcd:RPI1 seq:CACATCACGATC
-CACATCACGATCTGAGAATAAGAACATACATAA
-+
-JBFHHHIIJIJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9224:2207 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATCGTAAAAACTTTGGGATGC
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9118:2208 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTATAGTTCAGTCGACATGAAT
-+
-IJJJJJJJJJJJCCCFFDFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9087:2209 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATATGGATGGATAATTTTCT
-+
-IJJIIJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9013:2211 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAGGAGCCTCTGTAATTTTGT
-+
-JJJIJJIIGIJJ at CCFFFFFGHHFHJIGIJJG
- at HWI-ST960:105:D10GVACXX:2:1101:9153:2219 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCTCTTCGAATGACGAGTTCC
-+
-JJJJJJJJJJJJC at CFFFFFHHHHHJJJGIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9188:2234 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCCTTTGTCGCTAAGATTCGA
-+
-HIIIIJJJJJJJCCCFFFFFHHHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9022:2234 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTAAAATAAACACATGTACTT
-+
-HJJJJJJJJJJJCCCFFFFFHHHHHJJJHJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9098:2234 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCGAGGAGAGCAGTCTATTCTG
-+
-FFHGEHGIJJHI7@@FFFFFGHHHHIIJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9115:2236 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTGTTTAGTTGGCGGTTTCAC
-+
-IJJEHHFFFFFE at BCDFFFFHHHHHJJGHJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9136:2239 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTTTGCTTCCTTTAACAAAA
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9346:2162 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTCNCATGTCACATGAACGA
-+
-HHIJJIJJJJJJBC#4ADFDHFHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9443:2167 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCANATTAATCGAACTAAAGAA
-+
-IJJJJJJJJJJJCC#4ADFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9477:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATTTATGGCACAACATGTAA
-+
-IIJJJJJJJJJJ at CCFFFFFHFHHHJJJJHHJ
- at HWI-ST960:105:D10GVACXX:2:1101:9421:2187 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCCCAGCCTCATAGAGGAACTG
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9299:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCACCAAACTTTTCAAACCATGT
-+
-IJJHJIJJJHIJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9456:2199 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAATTTCGGAAATGCTAATCG
-+
-IJJJJJJJJJJHCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9347:2201 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGCATAATAATGTATTTATTTG
-+
-HJJJJJJJJIJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9436:2206 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTTATGAGTGTGCGTCTCAC
-+
-IGIIJJJJJJJJBCCFFFFFHHFHHJIIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9384:2226 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTCTGTTACACGCCGAGATC
-+
-IGIHHHHHHFFFCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9328:2231 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCACTGTTGCAGTCGGTGTTAT
-+
-IEIIJJJJJHHHCCCFFFFFHHHHHJHGHIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9477:2238 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTATGTGTGCTGCTTTCTCT
-+
-IIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9580:2160 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTNTCTACTTGTTCTGGCCT
-+
-HIIIIIIIIHII@@#4ADFDFHHHHII at GHII
- at HWI-ST960:105:D10GVACXX:2:1101:9707:2161 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTANGGAAATGTGCTATGGAC
-+
-IJJA;FHIGJJJ@@#4ABDDHGHHHGHFGHII
- at HWI-ST960:105:D10GVACXX:2:1101:9631:2165 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTNGAATAATGCGTTTGTAT
-+
-JIJJJJJJJJHHCC#4ADFFHHHHHIJJJHIJ
- at HWI-ST960:105:D10GVACXX:2:1101:9722:2167 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAANTCCACATGTTCAAGATT
-+
-IGJJJJJJJJJJCC#4ADDFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9563:2176 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCCTCGACACTGTTACTCCAC
-+
-JJJJJ(=EHHHHCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9614:2178 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATTGTCATATTTGCGATGTAT
-+
-IJJJIHJJJJJJCCCFDFFFHHHHHIJGIGGHC
- at HWI-ST960:105:D10GVACXX:2:1101:9676:2191 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTTTAAATCATTGTCTGAATT
-+
-IJJIJJJJJHJJCCCFFFFFHHHHHJJJJIIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9526:2191 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAATCTTTTGTATTTTGCTGT
-+
-JJJJJJJJJJJJCCCFFFFFHHHGHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9622:2195 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCTGTACCTGTTATGCTTTAAA
-+
-HJJIGHGGGIJJ@@@DDDEFDHHDHIIIJJIJI
- at HWI-ST960:105:D10GVACXX:2:1101:9597:2203 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAGTAGCTGTGGAATGAAAGT
-+
-IHJJJJJJJJJJCCBFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9507:2209 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTCTAGAGCTCTGATGAGTT
-+
-IIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9613:2210 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCTTTTCATAACTCATCCTACT
-+
-IGIGIJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9741:2245 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTATGAGACTGTATCCTTTAT
-+
-JGJJJIJJIIJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9572:2247 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTATTAAAATTAGAACAAAT
-+
-JJJJJJJJJJJJCBCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9606:2249 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTACATATAGTAGTGGAGGCCT
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHIJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9767:2159 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAANCCATCGGCTCCTTCTTTC
-+
-HJJJJJJJJGHHCC#4ADFFHHHHHJJJIIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9910:2161 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTCNTTCTCTCTAGTTTGTTT
-+
-IJIJJJJJJJJJCC#4ADDFHHHHHHIJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9952:2162 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAANACATCTTGTAGACTAAA
-+
-IHJJJJJJJJJJCC#4BDFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9830:2163 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTNGTTTCGAAGATCAATAC
-+
-IJJJJJJJJJJJCC#4ADDFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9980:2165 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAGNTTTTCTATATTCTTACT
-+
-IHIJIGJIJJJJ@@#4=ADDDFFHHJGGHIIE
- at HWI-ST960:105:D10GVACXX:2:1101:9995:2170 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTATGGGAACTCTTTTGGACC
-+
-JJJFIIGGGHIJ@<@FFDDDFHHFHJIGEHIG
- at HWI-ST960:105:D10GVACXX:2:1101:9998:2188 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATCTTATTAGTTTTAACTTC
-+
-IHIIIIIIJJJJ@@@FFFDFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9771:2192 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCCCTATAAATAAAAAACAGAC
-+
-JGIGIJJHHHHHCCCFFFFFHHHHHJJJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9841:2194 1:N:0: bcd:RPI1 seq:CACATCACGATC
-CACATCACGATCTACACCAAACTCTGGTACAGT
-+
-GCGGGHGJJIJJCCCFFFFFHHHHHJJFHIJJI
- at HWI-ST960:105:D10GVACXX:2:1101:9751:2194 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAATTGTTGTAGGCTGTGGTCC
-+
-JJJJJJJJJJJJBCCFFEFFHHHGHJJIJJIII
- at HWI-ST960:105:D10GVACXX:2:1101:9885:2199 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTATGTTTGTGTAACTGTAAC
-+
-IJJJIJJJJJJJ at CCFFFFFHHHHHJJJIIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9758:2211 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTTGGCGACTTTCTACCGCAC
-+
-IHHEHDEF at CEE@@@<DDADHHHDHIIIIIIEG
- at HWI-ST960:105:D10GVACXX:2:1101:9838:2213 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTGTAGCTCCATGAACAAAT
-+
-GGHEHIJJJIJJ at CCDFFFFFHGBFHIIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9815:2214 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTAATAAACACAAAAGTTTT
-+
-HIJIJJJJJJHHCBBFFFFFHHHHHJJJFHJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9945:2214 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCAGGATTGGTTTGGTGGATTA
-+
-HIJJJJIJJJJJB at CFFFFFHFHHHJCGIHJJI
- at HWI-ST960:105:D10GVACXX:2:1101:9878:2215 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTGAAGCCAGATCAGAATCTT
-+
-FGFHIHIIIIIIC@@FFFFFHHHDBFHGIGGHI
- at HWI-ST960:105:D10GVACXX:2:1101:9912:2218 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCAAAGTTAATTTCTGTTTCT
-+
-HIJJJJJJJJJJCCCFFFFFHHHHHJJHJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9753:2227 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTTACCAAATAAGCTTAAGTC
-+
-IJJJJJIIJJJJCCCFFFFFHHHHHJJJJJJHH
- at HWI-ST960:105:D10GVACXX:2:1101:9999:2231 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCTTTGTGATATCTGAAAAACAT
-+
-IJJJGIJJJJJJCCCFDFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9840:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTGATTTTTCCTTTGTTATC
-+
-IJJJIJJJJJIJBBBFFFFFHHHHHJIIIIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:9928:2239 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTGCAAAGGCAAGGCTCTGCTG
-+
-IJJIGJJGIJIICCCFFFFFHHHGHJJJIJGIE
- at HWI-ST960:105:D10GVACXX:2:1101:9937:2249 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAGTCGGCTTAACTAAGGTGGA
-+
-IIIEGGIHFHHH?@?BDDDFGHHGHHIEGACGH
- at HWI-ST960:105:D10GVACXX:2:1101:9908:2249 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAAGAACTCTGTAATTTCTGT
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10110:2162 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTNTGAGTTTATATTTCGGA
-+
-HHJHIJJJJJHHCC#4ADFDHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10222:2164 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTNAGACTTGGTCCCTAACAT
-+
-JJJJJJJJJJJJCC#4ADFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10062:2166 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTNCTGTACTCATTATCATCT
-+
-JJJJJJJJJIJJCC#4ADDFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10017:2167 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTNCGAACAATGAACAATTGC
-+
-HIIGIIIIIEHH?@#44BDBHH??FHBHIDDHI
- at HWI-ST960:105:D10GVACXX:2:1101:10129:2182 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTTGTCCTTAATTCATTTAT
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10012:2196 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTTTGTATCCTTTCTCATTTA
-+
-HIJJIJJIIIII at CCFFDDFHHHHHJJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10236:2203 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATATCACCATGTTCCAATTTC
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10124:2225 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAGTGTTGGCATGGGCCTCGA
-+
-IJJJJIJJHHHHCC at DDFFFHHHHHJJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:10018:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTCGGTTGACTGGAATTATTTT
-+
-IJJJJJJJHHGHCCCFFFFFHHGHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10188:2243 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTTGTGATTGTTGGCAATAT
-+
-HGIIIJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10113:2246 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTAAGTGTAGAATGCATAC
-+
-IGHIIJJJJJIJ@@CFFDEDHHGHHJJIJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:10362:2160 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTCNGGACTGGAGTTTGACTCT
-+
-IJJJJJJJIJJICC#4ADDFFGFHHGHEHJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10363:2184 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTGGATTCTTCGTTCAGGCCAT
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10329:2196 1:N:0: bcd:RPI3 seq:CACTTAGGCATC
-CACTTAGGCATCAAGACTGCAACAACTTCTGC
-+
-JGHIIIJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10309:2198 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTCTTCTGTCATCTACATATGC
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10373:2200 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAGTACTGTATTTGCTATTCCC
-+
-IJJIHJJJJJJJBCBDFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10440:2212 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCTTTTCTTTTTGTCGGCATC
-+
-C7CFGEGIIHHE@@CFFFFFHHHHCFGHIIII
- at HWI-ST960:105:D10GVACXX:2:1101:10352:2213 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTATTATCTCTGTTGATTGAT
-+
-HJJJJJJJJJJJCCCFFFFFHHHHHJJJIJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:10470:2218 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCCTAGAACTTGCTCAAAAAA
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10322:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCACTGGAACTCTTTCTTCTAA
-+
-IJIFIJJJIJJJCCCFFFFFHGHHHJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10300:2236 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGAATCCATAGTCTTACCATGA
-+
-ICHJJJJJJJJICCCFFFFFHHFHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10348:2237 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTATGACAAGTCGAATCTATT
-+
-IIJJJJJIJIJJ@@CFFFFFHHFHHIJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10434:2240 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTATGTCGTTTCTTTGAACT
-+
-GDFHIIJJJJII@@@FFDDAFFHHFIJGJJII
- at HWI-ST960:105:D10GVACXX:2:1101:10326:2249 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAAGAGTTGATTGTGCAAACAA
-+
-HGH>HH?GCEHG@?@DDBBDBHHFHGIIIGEHI
- at HWI-ST960:105:D10GVACXX:2:1101:10530:2160 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGATCCTNGTGATCATGAAAAAAAA
-+
-IHHGHHF at CFFFBC#4=DDFHHHGHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10666:2165 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTANCTCTCCAGTTTGTCATCT
-+
-FHHIIJHEEHGI at C#4ADDFHHHHHJJGHGGHJ
- at HWI-ST960:105:D10GVACXX:2:1101:10737:2166 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTNTGCTTATGTGCCCGTTTT
-+
-JJJDHIJHHHHHCC#4ADDFHHGDHIJJJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10690:2167 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATNTAAATTTCGGAAATGCT
-+
-JJJ>@GHGGHHHCC#4ADDFFHHGFGIGGIIJ
- at HWI-ST960:105:D10GVACXX:2:1101:10707:2172 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTATTTAAATTCCTTCAAGT
-+
-JJJJJJJJJJJJCB at FFFFFHHHHGJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10553:2176 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTATGTGTAGACTTAATTTTTT
-+
-HIJGIHHHFFFF at CCFDFFFHHHHHIIJJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10597:2193 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTAATGTACCGATGCATAGTC
-+
-IJJJJJJJJJJJBBCFFFFEHHHHHJJJJJJHH
- at HWI-ST960:105:D10GVACXX:2:1101:10566:2195 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTAGTTTTTGGATTGTAAATT
-+
-IJJJJJJIJJJJCBCFDFFFHHHHHJJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10694:2196 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTTGTAATGTTAAATAACTC
-+
-HIJIJJJJJJJJBB at FFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10746:2198 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTAACAGGGACAGTCGGGGGGT
-+
-DDDDDDDDDDDDCCCFFFFFHHGHHIIJJJJD:
- at HWI-ST960:105:D10GVACXX:2:1101:10522:2206 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTCTGTACAGATATACTTTTT
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10609:2213 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATTTGGCTTTTCTCTGCT
-+
-GIJGIJJJJIJJCCCFFFFFHHHHHJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10672:2216 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTTGGACTCGGATACGCTTCA
-+
-IIJJJJJJJHHH at CCFFFFFHHHGHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10584:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGATGTTGAGGCTCAAAAGTT
-+
-HIJJJJJJJJJJCCCFFFFFHHHHHJJJJIII
- at HWI-ST960:105:D10GVACXX:2:1101:10743:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTCGATAGAACTACAAAGAAT
-+
-IJJJJJJJJJIJCCCFFFFFHHHHHJJJIIIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10653:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTGTCCTTCGGATCACTCAAT
-+
-IIJJJJJJJJJJCCBFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10642:2240 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAGATTTTAAAGTGTTACAAG
-+
-IJJGEIJIIJIJ at C@DDFFFHDDHHGGJIIJG
- at HWI-ST960:105:D10GVACXX:2:1101:10627:2242 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAACAAGTTGGTCTGGGTTGT
-+
-IJJJJJJJJGHHB@@FFFFDFFDFFIIJFGHG
- at HWI-ST960:105:D10GVACXX:2:1101:10734:2245 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTAATCTGGGATGAACTCAC
-+
-HEHIIGIJJJJJC at CFDFFFHHHHHIIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10579:2247 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAATCTTTAGTAGAACAAAATC
-+
-IIJGIJIDIJJJ at CCFFFFFHFFFHIGHIIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10596:2249 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGGTACTAATGGCGAAAGAAC
-+
-IIJJJJJIIHHH at C@DFFFFHHHHHJJJGGGI
- at HWI-ST960:105:D10GVACXX:2:1101:10939:2167 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCANTAATTCCCTCTGATTCAT
-+
-HHHIIJGIJIJJ@@#4ADDFFHHHFGHJJJGJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10984:2173 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATTACGATGTCTCTGTACTC
-+
-IJJJJJIJJJJJCCCFFFFFHGHHHJJGHIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10870:2185 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATGGGTTCGACGTTAAAAAA
-+
-JJHHHHHFFFFFBCCFFDDFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10979:2195 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAACTGAAATGAACCAAAACC
-+
-HHIIIIIICEGHCCCFDFFFHGFHHJJJJJJH
- at HWI-ST960:105:D10GVACXX:2:1101:10780:2199 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTTGGTGGAACTACATTATC
-+
-JJJJIJJJJJJJCCCFFDFFGHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10858:2207 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGTTTGCGGATTATGCGTTTT
-+
-HHHHHFFFFFFECCBFFFFFHHHHHJJJJFGIJ
- at HWI-ST960:105:D10GVACXX:2:1101:10924:2209 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAACAAAGTCGTTGTAGTATAG
-+
-JJJJJJJJJIJJCCCFFFFDHHHHHHIJFHJJI
- at HWI-ST960:105:D10GVACXX:2:1101:10881:2211 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCATACTGTGTCTGCTTCTAT
-+
-IGIIIIIGGHII@@<DDFFEHHHHGIIBHIGI
- at HWI-ST960:105:D10GVACXX:2:1101:10798:2212 1:N:0: bcd:RPI2 seq:CACCGATGTATC
-CACCGATGTATCAATGTAGGTTGTTTTTGGAC
-+
-IJJJJJJHHHHH at CCFFFFFHHHHHJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:10962:2219 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTATAGGAATCTGTAACTTT
-+
-IGHIJIGIJJJJ@@@FFFFFHHHHGIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10898:2220 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTAATTTCGGCTGTAGCATGT
-+
-HIIEFHIIIIIJCBBFFFFFHHHHGEHIIIJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:10771:2225 1:N:0: bcd:RPI1 seq:CACATCACGATC
-CACATCACGATCGAGAATGATGAACCAATTAG
-+
-IFGHHHIJIGJICCCFFFFFHGHHGJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10861:2226 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTTGTTAGACTCTTCGATTT
-+
-JJJJIJIJJIJJC at CFFFFFHGHHHJJJJHIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10883:2230 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAAATGTTCTCTTTCTGATTT
-+
-JJJIJJJJJJIJ at CCFFDFFHHGHHIJJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10793:2238 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAACTAATGGATGTATGAATAT
-+
-HIJJJJJJJIIJCCCFFFFFHHGHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10996:2241 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTTTGTGTTGTTGACTCTGT
-+
-IJJJIJJJJJJJCBCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10908:2243 1:N:0: bcd:RPI2 seq:CACCGATGTATC
-CACCGATGTATCTGGAATGATGATAACGATTTT
-+
-IIJJJJJHEHHHCCCFFFFFHHHHHJJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:10822:2244 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGTGTGTCTCAGAAAAAAAA
-+
-HGHHFHHFFFFF at C@DDFDDHHGGFGGIIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11036:2163 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTCNATACAAGGACTGATTTT
-+
-IIJJJJJJJJJJCC#4ADFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11235:2165 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGNGTCACTGTTGTTGTTCTT
-+
-IIJJJJJJJJJJCC#4ADDFHHGHHJJJIJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:11150:2169 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTTGTAGTAACTGAAAACGG
-+
-JJJJJJJJIJJJCBCFFDFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11176:2178 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTCTGTTGACCAAAAAAAAA
-+
-FEFFFFFEEEEECCCFFFFFHHHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11080:2183 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTCCATAAGCTTTGATCACT
-+
-JJJJJJJJIJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11039:2186 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTAGTTAGTTGTTTTAAAAAA
-+
-JJJJIFHJJGHH@<??DFFDHHDDHJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11213:2190 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCAATAAGAATAAGAATAAGA
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11039:2203 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAGAGAAAATGAGCATTATTAT
-+
-IIIGIJIIGHIJCC at FFFFFHHHHHJEEHEHJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11145:2212 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTATGTTGTCTCTTAATCGGC
-+
-HJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:11168:2217 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAATCAATGCTGGTGCTAACTT
-+
-HJJJJJJJJJJJCCCFFFFFHHGGDHIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11088:2218 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAAGAACAAGAACACATTTAC
-+
-IJJJJJIJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11184:2224 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCACATCCTTTCAAAACAAGTTC
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJIIJ
- at HWI-ST960:105:D10GVACXX:2:1101:11073:2233 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTAAGTCTGGAATAGCTTTT
-+
-IJJJJJJJJJJJBBCFFDFFHHGGHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11102:2235 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATTTGTCGAACTTGTAAAAAA
-+
-JJJIJJJHHHGHCCCFFEFFHHHHHJEHIJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:11129:2239 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGGTTGGTTATACACCAAACTC
-+
-IJJJJJIJJJJJB@=DFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11163:2245 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTAATATGTCTGGCTTGTTT
-+
-IJJJJJJGIJJJC at CFFFFFHHHHHJJJJJGIJ
- at HWI-ST960:105:D10GVACXX:2:1101:11431:2161 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCCGNCTTTGACTTGAACCATAC
-+
-HJIJIJJJJJJJCC#4ADFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11339:2162 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTNATAGGATATCAATAAAAC
-+
-JIIJJJJJJJIJCC#4ADDFHHHHHJIIIJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:11265:2164 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTNGGTCAATAGTAGATACTT
-+
-IJJJJJJJIGHJ@@#4ABDFHHHGCGEIFIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11288:2167 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCTANATCTTCTTTTCAAATTTC
-+
-HJJJIJJJJJJJCC#4ADDFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11397:2167 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATNCCAGACGGCAAGTGTGA
-+
-JJJIJJJJHHHHCC#4ADDFHHHGHJJHIHJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11321:2204 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAAATCTGTTTGGTTGTGGAA
-+
-JGJJJJJJJJJHCCCFFFFEHHHHHIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11427:2204 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCTTCTTGGTAAAGGTTGAGT
-+
-IJJJJJJIJJJJCCCFFFFFFHHHHICGHHIJ
- at HWI-ST960:105:D10GVACXX:2:1101:11305:2204 1:N:0: bcd:RPI2 seq:CACCGATGTATC
-CACCGATGTATCTACTGACCCCGAGGCTTTCGC
-+
-HHHEFFCC;>>C@@@FDDBDFFHGGIIIIJHGH
- at HWI-ST960:105:D10GVACXX:2:1101:11259:2205 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAATATGTTTCGTAGAACTAT
-+
-IIIJGIJJJIJJCCCFFFFFHHHHHIJJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11401:2214 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTGTAGAAAATGAACTATAAAT
-+
-IJJIJJJJJHIJCCBFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11352:2220 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATTGAATAGTCGGGGTTACTT
-+
-IJJJHHHHFDFFCCCFFFFFHHHHHJJHIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11437:2220 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATTGCGTCGTATGAGTAAAAG
-+
-JJJIJJHHHHHF at CCFFFFFHHHHHIJGIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11258:2232 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAACCGAGTACTTTTGGTAGC
-+
-HIJJHIJIJJJJ at BBFFFFDHHHHHJJJFHIJ
- at HWI-ST960:105:D10GVACXX:2:1101:11443:2243 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTATGTAGTGTAGTGGTAAAA
-+
-JGIJJJJJJJJJ at CCFFFFFHHHHHIJFHJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11272:2245 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAGTGCTTCAACGGCTCTGGT
-+
-HIJJJJJJHHHH@@@DDFFFHGHFHIHGIIJH
- at HWI-ST960:105:D10GVACXX:2:1101:11399:2247 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGATCATATGAACTACGTGTGGCTT
-+
-JJJIJIJGIIJJCCCFFFFFHHHHHJHIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11695:2166 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAGNGCTTCCTAGAGCAAAGGA
-+
-IJJJJJJJJJJJCC#4ADFFHHHHHJJJJJJHJ
- at HWI-ST960:105:D10GVACXX:2:1101:11611:2171 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAGGAGCTCAAGAACGGAAGAT
-+
-IIJJJJJIJJHHCCCFFFFFGHHHHJJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11736:2174 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGAATACTGTGGTTGTTTTAG
-+
-JIJJJJJJJJJJCCCFFFFFHHHHHJHIJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:11736:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTGATACAATTTCGGTTTCGT
-+
-JJJIJJJJJHHHC at CFFFFFHHHHHJHIJJIH
- at HWI-ST960:105:D10GVACXX:2:1101:11623:2201 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTGTTTTGGGGTTTTAAACAT
-+
-IJJJJJHHHHFFCCCDFFFFHHHFHIJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11724:2214 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTTAGGACAGTTCATGTTTTT
-+
-JJJJJJHHHHHFCCCFFFFFHHHHHJJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11676:2225 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGCATCAAGCTGTAACCGAAC
-+
-HJJJJJIJJHHHCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11707:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGGTATGAACTATGAACACAA
-+
-IJJJJJJJJJJJCCBDFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11640:2237 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTTGTTAGACTCTTCGATTT
-+
-HHJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11532:2244 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCACTAGTAATAGAGCTTGGAA
-+
-IIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11511:2247 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATTGGAGATATTGGTTAACT
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJIIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11573:2247 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAACAATTCGGCTAGAAATTT
-+
-IGIJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11924:2158 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTNCGTCGTTGTAGAATATC
-+
-IIIJJJJJJJJJCC#4ADDFHHHHHJJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:11984:2158 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCACNACCATCTCTGAACTCAT
-+
-JJJJJJJJJJJJCC#4ADFFHHHHHIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11822:2166 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTNATTTTTTCTTGCAACAC
-+
-JJJJJJJHHHHHCC#4ADFFHHHHHJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:11773:2169 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCTTTCTTACTTCGGCCTGTT
-+
-JJJIJJJJJHHHCCCFFFFFHHHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11943:2187 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAAGATCATATGGACGTAACAT
-+
-IJJJJJJJJHJHCCCFFFFFHHHHHJJJJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11759:2191 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATTGAGCTCTTCTTTTCTTA
-+
-JJJJIJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11857:2196 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTCTGTAGTAGGCTTGCATGC
-+
-HHIIJJIIJJJICCCFFFFFHHHHHJJJJJJEH
- at HWI-ST960:105:D10GVACXX:2:1101:11838:2200 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTATCAATGTATTGTATCCG
-+
-IIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11790:2208 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTGAATTTCTGTAGACTATGT
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11770:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGGATGCGATCATACCAGCAC
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11869:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCTGATGTTGGTTTGTAATAT
-+
-IJJJJJJJJJJJBCCDFFFFHHFHHJIJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11959:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTACTGTACACACAAACTTC
-+
-JJJJJJJJJJJJCBCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11892:2215 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAATAAAATGACTCTGAAAAA
-+
-JJIJJJJJJJJJBCCFFFFFGHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:11899:2234 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTATAATGTAATAGTACTCACC
-+
-IJJJJJJJJGHJ at BCFFFFDHHHHHHIJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:12145:2162 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTGNTTCCGTTCCTGTTATCT
-+
-III<==8=8 at DI?<#4=BDD:<CDDEBEE9<D
- at HWI-ST960:105:D10GVACXX:2:1101:12229:2166 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAGNACTATTTGGGCTAAAAA
-+
-JJJJJJJJJJJJCC#4BDFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12088:2170 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCTTTTGTACAAATCCAAACCT
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12143:2181 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCTTCTGTCAACCTCTTCGGA
-+
-IJJJIJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12198:2193 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCAGGGATGATGATTCAATTA
-+
-HIJJIJJJJJJJCCCFFFFFHHHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12019:2199 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCATTGTTGAACTTAGAATCAA
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12174:2199 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTCTGTAGCTCTAGACCATTC
-+
-JGIIJJJJJJJJ at CCFFFFFHHHHHJJJIJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:12126:2204 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTATTCCCGTTGAGAGGATCAT
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12157:2207 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTGCTACTCTCCTCGTCTCCT
-+
-JGJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12048:2210 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTACCACTCTTGCATTTGCAT
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12070:2217 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCACAGAGCTCTGATTAAAGTG
-+
-JJJJJJJJJJJJCCCFFFFFHHHGHJJJJJHI
- at HWI-ST960:105:D10GVACXX:2:1101:12006:2219 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTAGTTGAGCGGTTGAATAC
-+
-IIJJJJJJJJHHCCCFFFFFHHHHHIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12122:2230 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTCTGTATGCTTTTTTGGGAC
-+
-==C@=@@A=777@@CFFDFDD<DFHGHIEHGEC
- at HWI-ST960:105:D10GVACXX:2:1101:12107:2231 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTCACAACCTGTGAAAATCT
-+
-HFHIGIJJJJIJCCCFFFFFHHHHHIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12066:2240 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTGTGGATGATGAAGAGTTTT
-+
-IIJJJJJJJIJJCCCFFFFFHHHGHJJIIGJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:12166:2250 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCTGCAATATTCTAAAGAACTC
-+
-JHJJJJJJJIJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12124:2250 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGAATTTGGATTTGATCAGTA
-+
-JJJJJJJJJJJJCBCFFFFFHHHHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12360:2161 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTNTAATTTCTATTTGGACT
-+
-IJIJJJJJJJJ)CC#4ADDFHHHHHJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:12436:2174 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTATAAAGTTAGTTGGTGGTTG
-+
-IJJJJJJJHHHHCCCFFFFFHHHHHJJGHIHII
- at HWI-ST960:105:D10GVACXX:2:1101:12303:2179 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATCTTTCTACTTTCATTAAC
-+
-JJJJGJJJJJJJ at BBFFFFDHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12490:2188 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCTTCAATTATGAGTTTTCCA
-+
-HIJJJJJJJJJJCCCFFFFFHHHHHHIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12308:2196 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGATCTATAGTTAAAAGAGCACTAA
-+
-JJJIJIG at HHIJ@@CFFFFFHHHHHJIJJIJG
- at HWI-ST960:105:D10GVACXX:2:1101:12371:2201 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTGGTTTGGACAAAAAAAAAA
-+
-C at CBBDDBC:ACCCCDFFFFHHHHHJJIJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:12329:2218 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGATCCTTTGTCGCTAAGATTCGA
-+
-JJJJJJJFHJIICCCFFFFFHHHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12376:2223 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCTGATCAAGTACAAGGGTTAT
-+
-JJJJJJJJJJJJCCCFFFFFHFHFHJIIJEGHJ
- at HWI-ST960:105:D10GVACXX:2:1101:12362:2226 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTAATATCGCATTAGCCCAGT
-+
-IIIIIIIIIIII@@@DDDD?FFFFAGIFFFF9F
- at HWI-ST960:105:D10GVACXX:2:1101:12430:2229 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTAATATACACTGAACTTTT
-+
-JJJJJJJJJJJJCBCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12484:2235 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTAAGTTTCTATCAAAAAAA
-+
-IJJJJJJJHHHHBBCFFFF;FHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12259:2237 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGCCTTGCTCTTCATTGGTTTC
-+
-HIJIIGIGIIIJ at CCFFFFFHHHHHJJIIIJHH
- at HWI-ST960:105:D10GVACXX:2:1101:12345:2240 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCCCGATAAATAGAACGATAT
-+
-JJJJJJJJJJHHCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12290:2249 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTTGTCTGAAAAAAAAAAAA
-+
-C at CBDBDBCDDCCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12543:2162 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCACNCGGTTGGTTTCCGTTAT
-+
-JIJJJJJJJJHHCC#4ADDFHHHHHJJJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12590:2166 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATNTGTATAAATAGTTTAAA
-+
-IIIJJJJJJJJJCC#4BDDFHHHHHJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12617:2173 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTAGTCTTATTGTATCTGT
-+
-IHIJJJJJJJJJCBCFFDEFHHHHHIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12673:2203 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTGATTCAAATCGATCCCT
-+
-IIJJJIJJJJJJC at BFFFFFHHHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12575:2204 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTTTATATTATGTGAAGTAC
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12730:2214 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTGAGTCGATCGTAGAGTCT
-+
-HJJJJJJIJJJJCBCFFFFFHHHHHJJIJHHJ
- at HWI-ST960:105:D10GVACXX:2:1101:12674:2224 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTTTGTTTGATGTCTATGAT
-+
-GFHIJGJIIJJJCB at FFFFFGGHHHJJIJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12690:2226 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCACTAGCTTCTACTTTGATAT
-+
-?9D:CHGHC787@@@DAD8DBFHAHIIB?<F?I
- at HWI-ST960:105:D10GVACXX:2:1101:12653:2228 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATTGTTTCTGTCTATGACTCC
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12702:2234 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAGAGCCTTGTTTCTTATTTT
-+
-IGIJIIJIJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12587:2240 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCTTATTGATGATTCTATCTT
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12614:2244 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTCGACATTTGGTGTGAAATGC
-+
-HJJJJJJJJIJHCCCFFFFFHHHHHIJJJJJHI
- at HWI-ST960:105:D10GVACXX:2:1101:12898:2157 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTNGTTAGTCGGACATCTTT
-+
-HIIJJJJJHHFHCC#4ADDDFHHHGJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12779:2159 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTNTAGGAATCTGTAACTTTT
-+
-IJJJJJJJJGJJCC#4ADFFHHHHHIIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12941:2162 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAANCCATCGGCTCCTTCTTTC
-+
-FGIIJGIGIJEHCC#4ADFFHHGHHJGIIIJJI
- at HWI-ST960:105:D10GVACXX:2:1101:12761:2162 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATNGAATTCAGAACTTTGTG
-+
-HIIIIIIIIIII@@#4=BDDHHHHHIIIIIIG
- at HWI-ST960:105:D10GVACXX:2:1101:12849:2171 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGCCCGACCTCGGACTGGGAAC
-+
-HHHHHHFFFFFFCCCFFFFFHHHHHJJJJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12894:2184 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAAAGTAGTCTCATCTTATCAC
-+
-HJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12816:2185 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTTAAAGGCTTATTATCAAAA
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12946:2186 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTCTGATGAAATCTCATATTGA
-+
-HJJJJJIIJJJJ@@BFFFFFHGGGHJJJJJJEI
- at HWI-ST960:105:D10GVACXX:2:1101:12964:2189 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCTAATATATGGACAATTTGGT
-+
-HGIIIJJJJJJJCCCFFFFFHHGHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12914:2190 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTATGTAACAACTTTTCATCT
-+
-IIIIJJJJJJJJCBCFFEFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12899:2205 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAAGAAAGTAGCATCAAAACAA
-+
-IJJHJIJJJJJJ at CCFFFFBFHFHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12750:2211 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCATCTAGTACATACTCTGTTT
-+
-JIJIJJJJJJIJCCCFFFEFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12962:2211 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTTTTGTCTGAGTACGAACT
-+
-JJJJJJIHJJJJCCCFFFFFHHHHFHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12876:2225 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTATAATTTTTAGTGAATAAC
-+
-IJJJJJJJJIIJBBBFFFFFHHHHHHIHJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12908:2229 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATTATGATGTAGAAGTATTG
-+
-IJJJJJIJJJJJBCCFFFFDHBFHHJJFHIJI
- at HWI-ST960:105:D10GVACXX:2:1101:12760:2229 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTTGGGCTCTTGTTGTGAATC
-+
-IIJIJIJJJIJJCCCFFFFFHHHHHJJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12926:2234 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTATTCAGCAGGATTATGCT
-+
-GHJGEIJJIJJIC@@FFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12942:2239 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTATTTCATTGTCTTGTCGGT
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJHIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:12902:2246 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTTATTTACATGTTGTTTGG
-+
-IGIHIIIJJJJJCCCFFFFFHHHHGIJIJJJH
- at HWI-ST960:105:D10GVACXX:2:1101:13152:2167 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGNAGAGCTGAAGAGCTTGAC
-+
-FGIIIGIIAGII@@#4ADDDFHHFFIBIIIICH
- at HWI-ST960:105:D10GVACXX:2:1101:13052:2176 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCTTTGTGACTGATCATTAG
-+
-HHJJJIIJJJJJCCCFFFFFHHHHGJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:13197:2180 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTTTGTCACATTGTAAATCCC
-+
-IJJJJJJJJJJJCBCFFFFFHHHHHIIIIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13235:2181 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTAATAAGATTTTCTAGTTG
-+
-IIJJJJJJJJJJCCCFFFFFHHHHHJJJJIGH
- at HWI-ST960:105:D10GVACXX:2:1101:13099:2185 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATTCTCTGTATCTCTCGACTCTCT
-+
-IJJJIIJJJGIJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13082:2187 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTAGTATTATTATACACACTTG
-+
-HJJIGIGGHHJJ@@@DDEFFHHFHDIJJIIIEI
- at HWI-ST960:105:D10GVACXX:2:1101:13132:2192 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTATAAATAAGCTTTGTTCA
-+
-JJJGGIJJJJJJCCCFFFFFHHHHHJGGGHGI
- at HWI-ST960:105:D10GVACXX:2:1101:13120:2196 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTAATTTGGACTGAGTCTGT
-+
-JJJJJJJIIJJJB at BFFFFFHHHHHHIHIHJH
- at HWI-ST960:105:D10GVACXX:2:1101:13177:2199 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCACTACGTCGTTTTGTTCTCTC
-+
-IIJJJJJJJJHHCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13060:2203 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAATTAAAGAAGAACCCAAAAC
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13106:2213 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTCGTAAACTCATAAATAAAT
-+
-IJJIIJJJJJJJCCCDFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13215:2231 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCACTGTGTTGGCGTTTTATCT
-+
-JJJJJJJJHHHHBCBFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13012:2238 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAAATGCCCATTAATCGTGGT
-+
-IJJJJGIIJJJJCCCFFFFFHHHHHJJJGHJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13172:2240 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTGCCTATTTATTTGCTGTC
-+
-HGJJIIJJJJJJCBCFFFFFHHHHHJHIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13045:2241 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTCTGAGATTGTAGAACAAT
-+
-IIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13155:2249 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCAAAAGGTCAAGGTTGGCAAG
-+
-IJJJJJJJJJJJBCCFFFFDFHHHHFHJJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13431:2158 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGATCGANGTTAGAACTCGAATCAG
-+
-GGJJJCGCHIJJCC#4ADDDHHHHHJJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:13336:2159 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTCNATCACATCTCCCTCTTGA
-+
-IJJJJJJJJIJJCC#4ADFFHHHHHJJJJJIJI
- at HWI-ST960:105:D10GVACXX:2:1101:13413:2164 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTANCAGTTGATAAATGAATAA
-+
-IGHGIIIIIIII@@#4ADADFHHHHGHIIIGII
- at HWI-ST960:105:D10GVACXX:2:1101:13458:2176 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTATGTAATGTAGTCTTTTAT
-+
-IIJJIJIJJJJJCCCFDFFFHHHHHIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13473:2178 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCGTTAGGACAGTTC
-+
-GHHGBDHII=BF@@@FFDFFHHHHH
- at HWI-ST960:105:D10GVACXX:2:1101:13435:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTGAATAATGAACTTTGATTAA
-+
-IJJJJJIJJGIJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13272:2183 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTAAATCTCCCTTTTTTTGT
-+
-JGIJJHHHHHHFCBBFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13312:2186 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTGTGTAGAATCTGCTTATAA
-+
-HIJIJJJJJIJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13253:2186 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATAGTTTGGACGTTGGTACACGA
-+
-IIIGIEEHGHHG@@?DDDFFFHHGABFBHIII
- at HWI-ST960:105:D10GVACXX:2:1101:13363:2187 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTGCTAAGGAAGTAAAAGCCAT
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHIJJIIIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13404:2208 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCACGACATTGCATTGTATGTTG
-+
-IJJJJJJJJIIICCCFFFFFHHHHHJIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13366:2209 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTATATGTTGTCGGTTCTAGT
-+
-FAFIIEHGGHAG@@@F=DFFBFFFHHIAHE<C
- at HWI-ST960:105:D10GVACXX:2:1101:13340:2212 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAATATGTTTCGTAGAACTAT
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13430:2220 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTATGTTTTGGATACATAAAC
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13478:2222 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCATGGTGATGAAACGAATATTT
-+
-IJJIJJIJJJHHBCCFDFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13253:2222 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTATGGGTCTCTAGATGCTTT
-+
-IJJJJJJJJJJJCCCFFFDFHHHGHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13357:2234 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGTCTTTGGTGCCCATGCAA
-+
-IIIIIIIIIIII@@@??DAB>F?DFACB?C?E
- at HWI-ST960:105:D10GVACXX:2:1101:13444:2236 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTTTACGATTCATGGTTCTGT
-+
-IHICBFHGIIII<@@FFBDDHDDHHGEHHBG?A
- at HWI-ST960:105:D10GVACXX:2:1101:13383:2241 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATAATCTCTACTGTTTGTTCT
-+
-FHIGIIGAGEHICC at FFFFFHHHGFHIGHCFEE
- at HWI-ST960:105:D10GVACXX:2:1101:13323:2243 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATTCTCAATACTTTCTTCCTC
-+
-HJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13571:2162 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTNTGTAGAATAAAGCTCTCT
-+
-IJJIJIIJJJJJCB#4ADDDHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13621:2162 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTNATATACACTGAACTTTT
-+
-JIJJJJJJJIJJCB#4ADFFHHHHHJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13664:2164 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGATCTTNCGTCGACTATGATTAAT
-+
-JJJJJJJGIJJJCC#4ADDFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13556:2177 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTTTGTATAAACGGAATTTCT
-+
-HIJIJJJJJIJJCCCFFFFFHHHGHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13647:2177 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCTTGATCACGAACATAATATT
-+
-HIJJJJJJJJJJCCCFFFFFHHHHHIJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13575:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAGCTTGCAAGTTCTCTCTGAA
-+
-JJJJJJJJJJIJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13528:2185 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATAGTATGTTTGCGGATTAT
-+
-IIJJJJJJJJJHB at BFDFFFHHHHHJJGIIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13614:2188 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTTCTTTCGAGTTTTATGAT
-+
-JJJIJJJJJJJJCCCFFFFFHHHHHJJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:13510:2190 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTGTCTTTCTCCTTCTCTTCT
-+
-JGIJJJJIJJJJCCCDFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13692:2200 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTGCTTTGCTTAATTCATTG
-+
-HIJJJJIJJJJJC at BFFFFFHHHHHJJJJJJH
- at HWI-ST960:105:D10GVACXX:2:1101:13666:2203 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTCAAATTTCAATGAGATTGT
-+
-IJJIJJJJJJJJCCCFFFFFHHHHHIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13720:2208 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATCAGAGTGACTCAACCAAA
-+
-IJJIJIIJJJJJBCCFFFFDHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13526:2209 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAGCCCTTTGTCGCTAAGATTC
-+
-JJJFJJJJIGFHCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13506:2209 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAATAATGTGTGTGGGACTTA
-+
-FHIIIIIIIIII@@@DDDD;CCFF;GFHHAEH
- at HWI-ST960:105:D10GVACXX:2:1101:13623:2212 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAATGGCAATCGTCTCTCTAT
-+
-IIJJJJJJJJJJCCBFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13684:2220 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTATGGTCCCCACTGAGAACT
-+
-IJJJIJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13646:2224 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTTTGTTATAGATTCCTCCT
-+
-IJJJJJJJJJJJCBCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13506:2227 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAGGAACAAGGATTACAAGAA
-+
-HIJJJJJJJJJJC at CFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13700:2234 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTATAAGCTGAGCGAATATTAG
-+
-IJJIJIJJHHHHCCCFFFFFHHHHHIJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13525:2242 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTGTTATTGGCCCAAGTAGA
-+
-HDHIIIJJIJGI at CCFFFFFHFFHHJIGCGGH
- at HWI-ST960:105:D10GVACXX:2:1101:13744:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTATGCTCTTTTAATGTGCAT
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJHJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13514:2246 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTTTTCAAACTGAGCAAAAAT
-+
-F=FDGIHGHGHG@@@DFDBDFHHDD:ACFHGHI
- at HWI-ST960:105:D10GVACXX:2:1101:13631:2249 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAGTTAATGTCTCTGAAACAA
-+
-IJJIJJJJJJJJCCBDFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13611:2250 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAACGTAGAAACTCTTGGTAA
-+
-JJJJJIJJJJJJCCCFFFFFHHHHHJJJJHIH
- at HWI-ST960:105:D10GVACXX:2:1101:13895:2161 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTNATGTTGGCAAAGAAACAC
-+
-IJJGIGHHJHHH@@#4ADDDHHHHFJGHIJIHH
- at HWI-ST960:105:D10GVACXX:2:1101:13803:2166 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCACNGTGTTGGCGTTTTATC
-+
-IGIJJIJJJJHHCC#4ADDFHHHHHIJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13821:2166 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTNCGTTCTCTGTTGATGAC
-+
-F=F;FADEEHGC@@#4=DDDFFHHFIF>C?EF
- at HWI-ST960:105:D10GVACXX:2:1101:13873:2169 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGGGGGTCCCAGTTCCGAACCC
-+
-HHHFFFFFFFEECCCFFDFFGHHHHJJJJJIIJ
- at HWI-ST960:105:D10GVACXX:2:1101:13832:2175 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTTGTGCCTTTTTCTCTTCT
-+
-HJJJJJIJJJJJC at CFFFFFHHHHHJJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13756:2181 1:N:0: bcd:RPI1 seq:CACATCACGATC
-CACATCACGATCACAGTCGGCTTACCCGGGGAC
-+
-DCFFEEEEDDDD at CCFFFFFHHHHHJJIIIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13888:2181 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTGAGAGATTTCGTAAAAAAC
-+
-IJJJJJJJHHHHCCCFFFFFHHHHHIJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13863:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTTGGTTGGTGTAAAAAAAA
-+
-HHHFFFFFEEEEBCCFFDFFHDFFHIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13978:2187 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTTGACTCTGTAGCTTTACTT
-+
-HHIHJJIJIIJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13770:2198 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCAACATATGTTTCATAATGT
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13874:2204 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCATAAAAGTTGTCGTAGCATAA
-+
-IJJIJJJJJJJH at CCFFFFDHHHHHJJJJJJHH
- at HWI-ST960:105:D10GVACXX:2:1101:13985:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCTCTTGACTTGCCTCCTTACC
-+
-HIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:13941:2214 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGATCTATTTATATATTTGATGTTT
-+
-JJJJJJJHIJJJCCCFFFFFHHHHHJJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:13963:2214 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTCTGTCTATTTCGTTAAATC
-+
-JJJJJJJJJJJJCCBFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:13752:2222 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCTTTGTCAATTGTCATATTTGC
-+
-JJJIIJJJJJJJCCCFFFFFHHHGHJJJJJJHI
- at HWI-ST960:105:D10GVACXX:2:1101:13859:2223 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTCTGTTTCAATGTCCCTTGC
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJ<4
- at HWI-ST960:105:D10GVACXX:2:1101:13939:2238 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAGAGTCAAGACTCAAGACTAT
-+
-IJJJJJJJJJJJBCCFDFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14150:2157 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCACNGTTGTAGTCTCTGTGTAT
-+
-HIJIJJJJJJJJCC#4ADDFHHHHHJJJHHHHJ
- at HWI-ST960:105:D10GVACXX:2:1101:14171:2160 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCGNATGAACTCTGGTTTAGTT
-+
-HHJHJJJJIJJICC#4ADFFHHHHHJGHJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:14041:2163 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCTANATATGTAGTCTTATGTCT
-+
-IJJHJJJJJJJJCC#4ADFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14084:2164 1:N:0: bcd:RPI1 seq:CACATCACGATC
-CACATCACGATCTCNGATGATGATCAAATCAT
-+
-HFHIFIJIIJIJCC#4ADDFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14180:2173 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCACAACAGCATATTTATAAA
-+
-FBF at GGIIGGHI@@@FFFFDHHBDHIJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14103:2174 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAACAAAAGTGGCTGTAGTTT
-+
-JJJJJJJJJJJJBCCFFFFFFHHHHJIJJGJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14196:2181 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTAGGTGTTACTGTGGATTTC
-+
-G4BFFHEHIHGE:==DD2BDHHBHDIEE at DGHE
- at HWI-ST960:105:D10GVACXX:2:1101:14128:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTAATGTAGTAGCAACTCTT
-+
-JIJJJJJJJJJJCBCFFFFFGHHHGJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14033:2191 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTGGTAACTGGACTCTGAT
-+
-HGIJJJJIJJJJC at CFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14074:2199 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTAATACACTTTCCCTTACAT
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14019:2201 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCTCTCTGTGATTCTCTTTTTA
-+
-HDGFHJIGJIGICCCFFFFFHHHHHIJJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:14232:2204 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAAGCTGGAAACTTTGAGCTT
-+
-IIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14143:2204 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTTGTGGCACACTAAGCTG
-+
-JGJJJJJJJJJJ at CCFFFFFHHHHHJJJJJI3
- at HWI-ST960:105:D10GVACXX:2:1101:14121:2210 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTCTAGTAGCATGTGAATTTA
-+
-IIIIIIIIIIII@??DDAD;?DHD?DDHGEGC
- at HWI-ST960:105:D10GVACXX:2:1101:14168:2213 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTATTCTATCGGATTCTCAAC
-+
-IGJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14102:2217 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTGTATTTGATCTACATTGTAT
-+
-HGHGIJIJIIGIBCBFFFFFGHHGHJIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14036:2225 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTCCCGAACTCTACGTAGAAAT
-+
-IJJJJJJGJJJHCCCFFFFFHHHHHJHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14209:2227 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTACTCAACACTCTCTTCTT
-+
-IIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14087:2229 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTGAGTTCTTAGCCATTGCAT
-+
-IGIJJJJJJJJJCCCFDFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14127:2230 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCACTCTGGATTCAATTTGGAT
-+
-JJJGIJJJJJIJ at CCFFFFDHHHHHJJIIJJI
- at HWI-ST960:105:D10GVACXX:2:1101:14273:2157 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTNCTCGTCGCTTGTGGCTC
-+
-H at EHIHHHHHHHCC#4ADFDHHHHHJFHIHIH
- at HWI-ST960:105:D10GVACXX:2:1101:14385:2158 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCGNGACAAAAGAACTGGACTC
-+
-IJJJJJJJJJJJCC#4ADDFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14449:2160 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTCNCTGTCACAATGGTTAAAC
-+
-IJJJJJJJJIJJCC#4ADDDHFHHHJIGIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14408:2163 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTNTGTTTTTCCCAAAATAC
-+
-HHJJJJJJJJJJCC#4ABDFHHHHHJJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:14427:2163 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTNACAGAAGATAGAGAGCAC
-+
-HJJJJIJJJJJJCC#4ADFFGHHHHJJIIJJGI
- at HWI-ST960:105:D10GVACXX:2:1101:14472:2172 1:N:0: bcd:RPI1 seq:CACATCACGATC
-CACATAACGATCCTCTGTGTCTCTCTCGATCGA
-+
-HHJJJIJJJJJHCCCFFFFFHHHHHJJJJJJ33
- at HWI-ST960:105:D10GVACXX:2:1101:14402:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAATAAAGTGGTCTAGTGGTT
-+
-IJJJJJJJJJJJCCCFFFFDHHHHHJIEGIHG
- at HWI-ST960:105:D10GVACXX:2:1101:14443:2185 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCTTTTACTGTCCTCTGATCAG
-+
-JJJIIJJJJJJJCCCFFFFFHHHHHJJJJJJ3
- at HWI-ST960:105:D10GVACXX:2:1101:14420:2208 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTATGTATATATAAGAGTCAT
-+
-IJJHJJJJJJJJCBCFFDFFGHHHHJJJJHHGJ
- at HWI-ST960:105:D10GVACXX:2:1101:14467:2209 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGAAACTGTACTTGAGATTA
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14311:2215 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTCTTTATGGCTCTAGTACAA
-+
-JIJJJJJIJJJJCCCFFFFFHHHHHJJJIIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14442:2218 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAAAAATGTCGTTGTAGTATAG
-+
-JJJJJJJJJJJJCCCFFFFEHHHHHHJJIIJGI
- at HWI-ST960:105:D10GVACXX:2:1101:14388:2226 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAATTCCAGTTGATTGAGGTC
-+
-ICHIHIFHIJJJCCCFFFFFHHHHHJGHJJII
- at HWI-ST960:105:D10GVACXX:2:1101:14404:2228 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGTTGTTGGCTATGATGTTAT
-+
-HIIJIJJJJJJJCCBFFFFFHHHHHIIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14361:2234 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAAATTATGATGGAAGATTTGT
-+
-HHJJJIJJJJJJCCCFFFFFHHHHGJJHJJJ34
- at HWI-ST960:105:D10GVACXX:2:1101:14303:2235 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCACATTTAGGCTCAGTGGGA
-+
-JIJJJJJJJIJJCCCFFFFFHHHHHJGHIIG
- at HWI-ST960:105:D10GVACXX:2:1101:14342:2235 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGCTCTTCAACCTTAGAAGA
-+
-IGJJJJJJJJJICCCFFFFFHHHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14263:2238 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTACTTTCTCGTGCTAACTC
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14722:2164 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTNGTTGGCCTTAAAAAAAA
-+
-EEHHEHFFFFFECC#4ADFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14632:2164 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGNTGATTCTCCTTAGATCTG
-+
-FHIIJJJJIIJICC#4ADDFHHHGHJJJJJJGI
- at HWI-ST960:105:D10GVACXX:2:1101:14512:2169 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGCAATCCCTCTGTTTCCTAA
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14677:2181 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTGACAGAAGATAGAGAGCAC
-+
-IIJJJJJJJJJJCCCFFFFFHHHHHJJJJIIGJ
- at HWI-ST960:105:D10GVACXX:2:1101:14738:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAATGTTCATGTCTAAATTCG
-+
-HHJJJJJJJJJJCCCFFFFFHHHHHJJJJJJ3
- at HWI-ST960:105:D10GVACXX:2:1101:14684:2203 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAAGCCGGAGACAGGAGAGGTG
-+
-HHHHFFFFEEEECCCFFFFFHHHHHJJJJJJ*?
- at HWI-ST960:105:D10GVACXX:2:1101:14526:2204 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCACATAGACTAATCTTATAAT
-+
-JIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14580:2206 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAAATAAGGTATCAGGTTTTA
-+
-IIJIJJJJJJJJCCCFFFFFFFHHHJJEHIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14592:2223 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTTATAGGGAGAAGAAGAGGC
-+
-HDHIJIJJJJHHCCCFFFFFHHHGHJJJIJJ34
- at HWI-ST960:105:D10GVACXX:2:1101:14659:2235 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAATTGGTGCCTGTAGGTCAG
-+
-IHJJJJJIJJJJCCCFFFFFHHHHHJJJFHI3
- at HWI-ST960:105:D10GVACXX:2:1101:14548:2237 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCAATTTTATGTCGTTTCTTTG
-+
-JJJIIJJJJJJJCCCFFFFFHHHHHIJJJJJ<
- at HWI-ST960:105:D10GVACXX:2:1101:14792:2167 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCTANGGTTTGGCTGTTAACAC
-+
-FBGE>FHIJJHHB@#4ABDFHHHHHIJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14962:2168 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAATCCACACTAAGTCCAAGC
-+
-HIJJJJJJJJJJCCCFFFFFHHHHHHIJIJJG
- at HWI-ST960:105:D10GVACXX:2:1101:14851:2171 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTATTTGTAGCAATTCTGTTTT
-+
-IJJJJJJJIIJICCCFFFFFHHHHHJJIIFHHJ
- at HWI-ST960:105:D10GVACXX:2:1101:14982:2172 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCGTAATCTGGGATGAACTCACT
-+
-JJJIJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14927:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATTCTTGTTTAGAAGCAAGAA
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:14906:2195 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGCCAACTCTGTTTCTTCTTCT
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJIJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:14858:2195 1:N:0: bcd:RPI3 seq:CACTTAGGCATC
-CACTTAGGCATCATTCGTTTCAATGTCAATCTC
-+
-IIIHGIHGIJJJ at BCFFDEFHHHHHIJJIJJII
- at HWI-ST960:105:D10GVACXX:2:1101:14936:2201 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAGCCAATGTTGTAGAACTAT
-+
-HIIIIIIIIIII@@CFFDFFHDAFFBHIG at H@
- at HWI-ST960:105:D10GVACXX:2:1101:14780:2204 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTTGTGAATCCTTTTCCATT
-+
-IGJIJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14808:2217 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAATGAAGAGGCTGTTTCTAC
-+
-IGIJJJJJJJJJCCCFFFFFGHHHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14828:2217 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATGTATGTTGTTATTTGATAA
-+
-HGIGIGIJHIJI at CCDFFFFHHHHHJJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14929:2217 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAACACTCTTATCAAAAAAAA
-+
-IJHHHHFFFFEECCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:14844:2223 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCATACATCTTTGCAGAACTCAT
-+
-HIIC=CGCFGIH at C@FFFDFHGFDFD<ABBDIF
- at HWI-ST960:105:D10GVACXX:2:1101:14988:2233 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAGCTTAGACTTGGTAGTTGT
-+
-HHJJJJJJJJJJCCCFFFFFHHHHHEHIHIIG
- at HWI-ST960:105:D10GVACXX:2:1101:14821:2236 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAGTGTACTTGTGGACAAGGT
-+
-FFHIHIJGHIJJ@@=DDEFFHHHHGJJJJJI>
- at HWI-ST960:105:D10GVACXX:2:1101:14761:2243 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATTTGTAGTCGTAAATATCT
-+
-IHJJIJJJJIJJCCCFFFFFHHHHHJIJIIII
- at HWI-ST960:105:D10GVACXX:2:1101:15012:2166 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAANTTCTCCCATCAGTTACAA
-+
-IIJJJJJJJJJJC@#4ADDFHHFHHJJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:15055:2167 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAGNAACTGTATCTATGTCGT
-+
-JJJJJJJJJJJJCC#4ADFFHHGHHJJJIIJG
- at HWI-ST960:105:D10GVACXX:2:1101:15030:2168 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTCTGTTACACGCCGAGATC
-+
-JJJHHHFFFFFECCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15079:2180 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTCAGGGCAAGCACAACATAT
-+
-JJJJJJJJJJJJCCCFFFFFHHGHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15143:2186 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCATCTTTTTCATCCCAATCTGT
-+
-HIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJ<3
- at HWI-ST960:105:D10GVACXX:2:1101:15178:2193 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAGTGATGAACCTTTTGAACC
-+
-IJJJJIJJJJJJCC at FFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15053:2195 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAATCCAGTCTCATCGCTGTTG
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJIJJJJEI
- at HWI-ST960:105:D10GVACXX:2:1101:15025:2214 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGATCGTATGTAAAGGTTTACTCTTT
-+
-JJJJJJJHIJJJCCCFFFFFHHHHHIJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15186:2216 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCAGAGCAAGTCGAAATCTGTT
-+
-JJJJGJJJJJJJCCCFFFFFHHHHHJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:15065:2224 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTGTGCTGGGAACTATTTGAC
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:15143:2225 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATGAAAACTTCTTGAGTTAT
-+
-IIJJJIJIJJJJCCCFFFFFHHHHHJJJIIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15008:2227 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCTTTCTTGGGACTTGATTTTT
-+
-IGIHIJHGHHFF#CCFFFFFHFHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15207:2236 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTAGTGTGTAATGTTATTGG
-+
-IIJIJJJJJJJJBCCFFEFDHHHHHJHJJJJ34
- at HWI-ST960:105:D10GVACXX:2:1101:15000:2247 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTTGGTCATGTTTGCTATTTG
-+
-FFF;FF at G3=DC at CCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15342:2165 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCCGNATCTGGATTTAAGATAA
-+
-IGIIIJJJJJJJCC#4ADFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15274:2198 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCATCTGTCTAAAGTTTGTTCT
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15308:2216 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAGTAATTTAGCATGTTGCAAA
-+
-IJJIIJJJIIJICCBDFFFFHHHHHJJJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:15475:2222 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTCTGTAGTTGTATTTCAAC
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15291:2232 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTATGTTGTTAGCTATCACT
-+
-IHJJJJJJJJJJC at CFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15347:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTGAACTCTGACCAATGAACTT
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15331:2245 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTGTTATATATTACTGACTAC
-+
-HJJJJIGIJJJJCCCFFFFFGHHHHJJJJJJDI
- at HWI-ST960:105:D10GVACXX:2:1101:15450:2248 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTGTTTTGTCCCTTTGTATTT
-+
-JJJJJJJJJJJJCCBFFFFFHHHHHJJHIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15610:2159 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTGNTCTGATTTCAATTTTTGC
-+
-JJJJJJJJJIJJCC#4ADFFHHHHHJJJJJI33
- at HWI-ST960:105:D10GVACXX:2:1101:15730:2162 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAGNCTGCTACAACAAAAAAAA
-+
-HHH>DFDDCEEDCC#4ADFFHHHHHJJJJJJIH
- at HWI-ST960:105:D10GVACXX:2:1101:15650:2166 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTNTTGGCAGCGTATCTTTTC
-+
-HIJJJJJJJJHHCC#4ADFFHHHHHIJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15745:2167 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTNATGTCATTAATGAAAACT
-+
-HIJJJJJJJJJJ@@#4ADDFGHHHFJJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:15691:2179 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTACTAGTCTCGTATTAACTA
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:15591:2179 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTTTGCTTATGTGCCCGTTTT
-+
-IIJJJJJJHHHHCCCFFFFFHHHGHJJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:15612:2183 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATATCCTATGTCTAAAAAAA
-+
-IIJIJJJHHHHHCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15528:2190 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCATTTCGGATCTTGGCTACTAA
-+
-IJJIJJJJHHHHCCCFFFFFHHHHHJIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15503:2198 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAATCTAAAGGGATTTGGTGT
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJHII
- at HWI-ST960:105:D10GVACXX:2:1101:15541:2201 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CAAACTTGAATCGTCTGTAGCTCTAGACCATTC
-+
-IIIIJJGIGIJJ at CCFFDEFHHFHHJIJGGIJH
- at HWI-ST960:105:D10GVACXX:2:1101:15700:2204 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTAAATTCTCTTCCTTTGGT
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJG
- at HWI-ST960:105:D10GVACXX:2:1101:15649:2217 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTAATGTGATGGTTTCTTCAA
-+
-IIJJJJJJJJJJCCCFFDFFHHHFHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15573:2222 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAATAGCTAGTCATAACTCTTT
-+
-IJIJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15731:2236 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAATATGTTTCGTAGAACTAT
-+
-JIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15639:2244 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCTTTTACGGAGTACAAGAGAT
-+
-JJJJJJJJJJJJCCCFFFFFHHHFHIJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15900:2158 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGCNAGATGATGGTCATTATAA
-+
-IJJJJJJJJJJJCC#4ADFFHHHHHIJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15963:2161 1:N:0: bcd:RPI1 seq:CACATCACGATC
-CACATCACGATCATNTGTAAATATACCACGAAT
-+
-C=GI@=CHC7=E@@#4==BDA?DFHG@<A<CCG
- at HWI-ST960:105:D10GVACXX:2:1101:15856:2161 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCTCNGATGATGATCAAATCAT
-+
-JJJIJJJJJJJJCC#4ADFFHHHHHJJJJJII
- at HWI-ST960:105:D10GVACXX:2:1101:15824:2174 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTATATGTCTGTACACAATCT
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15924:2187 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTATGAAAATGTTGTGAACTG
-+
-IIJJJJJJJJJJCBCFFFFFHHHHHJIJJJJGJ
- at HWI-ST960:105:D10GVACXX:2:1101:15857:2189 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCTTAGGTTTAGAGCTAAAAAA
-+
-IJJGJJJJJHHHCCCFFFDFHHHHHJJJJJJII
- at HWI-ST960:105:D10GVACXX:2:1101:15755:2216 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTATACTACTAATACATTTT
-+
-JGIIIJJJJJJJCBCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15970:2220 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCCATGACTGAAGTTGTTTGTC
-+
-IJJJJJJJJJIJCCCFFFFFHHHHHJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15886:2223 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTTGTTTTATTTCTTATTCAA
-+
-IJJGJJJJIJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:15866:2238 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCTGTGTTGGCGTTTTATCTG
-+
-IIJJJJJJJJJHBCCDDFFFHHHHHJJJJJJ2
- at HWI-ST960:105:D10GVACXX:2:1101:15925:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTTTTGTTGGATTGTTTTGCT
-+
-FFHBHJGIEA at C@@@FFEDDHGFBHBHIJGGGI
- at HWI-ST960:105:D10GVACXX:2:1101:15938:2248 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTCTTGTCCGTTACATTTGCC
-+
-IGIIJJJJJJJJ at CCFFFFFHFHFHJJJJJJG
- at HWI-ST960:105:D10GVACXX:2:1101:16121:2167 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTNATATATTCATGCATATT
-+
-IIJJJJJIJJJJCC#4ADFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16240:2167 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTNAGTAGTAGTAATGTCAAC
-+
-IIIIIECCFHII?=#4=DDDCFFFFHGHEEI at H
- at HWI-ST960:105:D10GVACXX:2:1101:16016:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCACTGTGTTGGCGTTTTATCTG
-+
-HIJJJJJJJJHHCCCFFFFFHHGHFIJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:16084:2189 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAAATGTGAAATCTTAAAATC
-+
-IIIC?==BFHII@@@DD:=DFDDB?ECDFGED
- at HWI-ST960:105:D10GVACXX:2:1101:16060:2193 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCGAGAATGATGAACCAATTAC
-+
-HJIIGJJJJJJJCCCFFFFFHHHHHJJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:16022:2204 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCATGAGATACTGAATTCAAGC
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJ33
- at HWI-ST960:105:D10GVACXX:2:1101:16131:2207 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTATGTATGATCATATTTTT
-+
-HIJJIJJJJJJJCB at FFEFFHHHHHJJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:16147:2216 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCATTCAAATCAGAGGCTTGTTA
-+
-FHIGIJIJIIFHCCCFFFFFHHHGHJJJJIFEH
- at HWI-ST960:105:D10GVACXX:2:1101:16171:2218 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTCTTCTTCGTTTGGCTATTTT
-+
-IJJJJJJJJHHHCCCFFFFFHHHHHJJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:16114:2220 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTGCAGCACTTGTCTGACCCAT
-+
-JJJJJJJJJIJJCCCFFFFFHHHFHJJJJJJII
- at HWI-ST960:105:D10GVACXX:2:1101:16083:2223 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAATGTAGAGAATCGATTTAT
-+
-JJJJJJJJJIJJCCCFFFFFHHHHHJJJJIJI
- at HWI-ST960:105:D10GVACXX:2:1101:16174:2241 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCACTTTGAGAACTAAAAAAAA
-+
-=7=7=E=7@###@@@DDDDDFFFFFIIIIIID
- at HWI-ST960:105:D10GVACXX:2:1101:16002:2242 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGGAGTTTTGGTTAGGTTGT
-+
-GHJJJJJJJJJJBCCDFDDFHHHFHIJJEHI:
- at HWI-ST960:105:D10GVACXX:2:1101:16214:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTTGGTAGATGATAACAAATC
-+
-HJJIJJJJIJIJCCCFFDFFHHHGHJJJJJJII
- at HWI-ST960:105:D10GVACXX:2:1101:16126:2245 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATTGTTGTTGTTGTTGTTGT
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHIIJIIJ;
- at HWI-ST960:105:D10GVACXX:2:1101:16191:2247 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCTGGAGAACTTGGCAACTCAC
-+
-IIIB=FHIIIII@@CFFFFDA?FFAHIIGEE@
- at HWI-ST960:105:D10GVACXX:2:1101:16292:2160 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGCNCTTGTTAGTAGTTTCTG
-+
-IGIJJJJJJIJJC@#4ADDDDHHFHJIIIJJ3
- at HWI-ST960:105:D10GVACXX:2:1101:16335:2161 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTANTCCACTTGCTTATCATC
-+
-HIIGHIJJJJJJCC#4ADFFHHHHHJJJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:16262:2167 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCCANTTGAGGAACTATTGTTT
-+
-C=CFHEEGHICA7;#44ABDHDDHDGG at EA@>
- at HWI-ST960:105:D10GVACXX:2:1101:16438:2169 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATGTTCGGTTGTGGGATTCT
-+
-HIJJJJJJHHHH at BCDFFFFHHHHHJJGJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16355:2177 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTTGTTAGACTCTTCGATTT
-+
-HGHJJIJJIJIJCCCFFEFFHHHHHJJJJJJGJ
- at HWI-ST960:105:D10GVACXX:2:1101:16306:2182 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTACCTACTCGTCGTACATTTT
-+
-HJJJJJJJHHHHCCCFFFFFHHHHHIJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16427:2183 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGTTGATTTTAATGGTTACTGT
-+
-BFHIJGHIEHII at CCFFFFFHHHHHJFHGHIIJ
- at HWI-ST960:105:D10GVACXX:2:1101:16368:2191 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATAAAAACTCTGAATTTAAT
-+
-IJJJJIJJIJJJCCCFFFFFHHHHHJJJJIJC
- at HWI-ST960:105:D10GVACXX:2:1101:16496:2191 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTTCTGTTGAACCTCTTG
-+
-HHJIIIIJJJIJCCCFFFFFHHHHHJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16268:2194 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTCAAACCATTGAGACAGCTT
-+
-HIJJJJJIJJJJCC at FFFFFHHHHHJJJJJJGI
- at HWI-ST960:105:D10GVACXX:2:1101:16478:2197 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCCTGTGAAACTGCGAATGGCT
-+
-F=FHIHJGIJJHCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16378:2215 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTACGTTATTTAAAATCCTC
-+
-IJIJJJJIJJIJCBBFFDFFHHHHHIJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16273:2227 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGTTATGTGACTGGAGAGA
-+
-IIJJJIJJJJJJCCCFFFFEHHHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16350:2227 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTGTGGCTCAGAACCACCAC
-+
-IIJHIJJJJHHHCCCDFFFFHHHHGJJJIJII
- at HWI-ST960:105:D10GVACXX:2:1101:16328:2230 1:N:0: bcd:RPI4 seq:CACTGACCAATC
-CACTGACCAATCACTGATCGCGTCGTGTTAC
-+
-HIJJJHHHHHFF at BCFFFFFGHHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16408:2232 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTTCGAACAATGAACAATTGC
-+
-HIJJJJJJIJJHCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16369:2234 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTACATTGTGAAATGATATTTC
-+
-HGEGGIJGIJJJ at CCFFFFBHHHHFGIIJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:16305:2250 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCAAACCTGTATCTGTGTAACT
-+
-IIJGIJJJIJJJCCCFFFFFHHHGHGJIGHIIJ
- at HWI-ST960:105:D10GVACXX:2:1101:16684:2159 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTNTTCGGATTTGAACAGA
-+
-JIIJJIJJJJIJCC#4ADFFGGHHHJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16513:2160 1:N:0: bcd:RPI5 seq:CACACAGTGATC
-CACACAGTGATCTGNTATGTTGGTTAAGACTTT
-+
-JIIIIII at C=DH at C#4ADDDFHHFHIJJJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16553:2167 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCACNGTTTTGCTAAAATATTC
-+
-HAHGIJJIJJIJCC#4ADDFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16647:2170 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTAATTGAATATCTTCAATGT
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16734:2178 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTACGAATTCTAAATTTTAT
-+
-HIJIJJJJJJJJBBBDFFDDHHHHHJJJJIIJ
- at HWI-ST960:105:D10GVACXX:2:1101:16682:2192 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTATCAATAAGCGGAGGAAAAG
-+
-HIIGHGGHHHFF@@@FFFFFHHAFFHDDHIIII
- at HWI-ST960:105:D10GVACXX:2:1101:16516:2203 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGAGAGTTCGAATCTGTCAGGC
-+
-GIJJJJJJJJJJCCCFFEFFHHHHHJJGIJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:16583:2204 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATCGGCGCTTGTTCACCTCTC
-+
-HIHHHHHFFFFFCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16633:2220 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCATTGTATTTTAACAGCACTC
-+
-JJJIJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16696:2231 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTATGTAATGTAGTCTTTTAT
-+
-GGHIIIJJIIJJ at C@DDDDFHFFHDBGIIIIH
- at HWI-ST960:105:D10GVACXX:2:1101:16666:2233 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCTTAACACTTGGTTCCGTTTC
-+
-IJJJJJJJJJIJCCCFFFFFHHHHHIJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16730:2240 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCCTATAAATCGTCTCATGAA
-+
-JJJGIJJJJJJJCCCFFFFFHHHHHJJJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16561:2240 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATAACCCTTTCCAGGCCATGT
-+
-CDHIGHIIIGCD@@CFDEFFHHDHHGFBHEGGJ
- at HWI-ST960:105:D10GVACXX:2:1101:16708:2243 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCACCATTGTCTGAATAAAAAG
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:17000:2158 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTNATCCTCGTTATATTTGT
-+
-FFFIIIIIIIFI==#4=2ADFAFFF at FIIE@C
- at HWI-ST960:105:D10GVACXX:2:1101:16900:2161 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGANCAAACCGACACTCGGGAT
-+
-HHHHFFFFFFEECC#4ADFFHHHHHJJJIJJHI
- at HWI-ST960:105:D10GVACXX:2:1101:16800:2165 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATNTATTTGGGGTTATTTGCA
-+
-HIJJJJJJJJJHCC#4ADDFGHHHFHIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16874:2165 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCTTNGTTGAACGACAAAATAA
-+
-GHIHEDEHHGFF at C#4=BBDHFHHGGIGJEGG
- at HWI-ST960:105:D10GVACXX:2:1101:16973:2166 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCACNGTGTTGGCGTTTTATCTG
-+
-IJIIJJIGIHHHCC#4ADDDHHHHHJJJIJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:16783:2167 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGGNTGTGCAGACTAAGGAGC
-+
-FFFIIIFIIIII@@#4=DDDFFFFFIIIIIII
- at HWI-ST960:105:D10GVACXX:2:1101:16847:2173 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCGATGTCGGCTCTTCCTATCAT
-+
-GIJJJJJJJJJJCCCFDFFFHHHHHJGIGIIIJ
- at HWI-ST960:105:D10GVACXX:2:1101:16809:2177 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCACATCCTCATAATCACTTTC
-+
-FDHJJEFIGIIJCCCFFFFFHHHHHIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16946:2180 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTCTTTTGTCGGCGTTAGGT
-+
-HHHHFFFFEEEECBCFFFFFHHHHHJHJJJJH
- at HWI-ST960:105:D10GVACXX:2:1101:16831:2183 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTATGTTATGGATTCAAAAAAA
-+
-HIJJJJJHHHHH at CCFFFFFHHFHHJIJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16770:2187 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTCAGCCCTTTGTCGCTAAGA
-+
-HIJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16858:2188 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAATTTTTAGTGACCCTTTTA
-+
-HIJJJIJJJJJJ@@@FFFFFHFFHHJIJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:16876:2193 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTATGTTCTCTGTTATTCTC
-+
-IIJJJJJJJJJJCBCFFFFFHHHHHJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16983:2194 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCTTTGTGGGTTGAGTTGTCT
-+
-HIJIJJJJIJHHBCCFFDFFHHHHHJHIJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:16842:2205 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTATGAAATCGACCATGACA
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16962:2210 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTCATGCTGTTTTCCAACAGC
-+
-IJJEIIJJJIGH at CCFFFFFHHHHHJJIJJJIJ
- at HWI-ST960:105:D10GVACXX:2:1101:16751:2219 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTACTGTTTTCTGTTTTCTT
-+
-JJJJJJJJJJJJC at BFFFFFHHHHHHIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16898:2223 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCAACCCCCGAACTATATCCTC
-+
-HIJJJJHHHHHFCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16969:2228 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCATTATCTTGTAGAATGTTCA
-+
-HGIJJJJJJJJJCCCFFFFFHHHHHJJJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:16781:2240 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTTCTCCTCTCGTCCATAAAT
-+
-IJJJJJJJJJJHCCCFFFFFHHHHHIJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:17176:2160 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGCNAGATGATGGTCATTATAA
-+
-GIJIJJJJJIJJ@@#4ADDFGHHHFGIJJIJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:17068:2161 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTNCACAAGAAAATCAAATAA
-+
-HIJJJJJJJJJJCC#4ADFFHGHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:17154:2164 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTNGTGGATGATGAAGAGTT
-+
-HII;@HGGHIII@@#44ADDFHHBFGEGGICF
- at HWI-ST960:105:D10GVACXX:2:1101:17222:2169 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTGGATCCTGTTTTGGATTGT
-+
-IIJIJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:17028:2180 1:N:0: bcd:RPI6 seq:CACGCCAATATC
-CACGCCAATATCCTATTTACTATTTGAAAAAGC
-+
-IJJIJJJJJJJJCCCFFFFFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:17127:2184 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCAATTGGACTGTTTAACGTTT
-+
-JGIJJJJJJJJJCCCFFFFFHHHHHJJJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:17143:2189 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCAAATTTCTATATATTGTTTT
-+
-JJJGGJIIGJJJ@@;DDFFFHGHHGJJJFHIJ
- at HWI-ST960:105:D10GVACXX:2:1101:17161:2201 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCTTCTGGACATTAGCCATTAGT
-+
-HIJJJJJJJJJJCCCFFFFFHHHGHIJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:17133:2206 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCTGCCTTTTCCTTCTTGTCGG
-+
-JJJJJJJJJJJJ@@CFFFFFHHHHHJIJIIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:17121:2224 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGGCACTTCTGTTCTGATCCT
-+
-JJJJJJJJJJJJCCCFFFFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:17033:2228 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCACTAGACAAACTCTCAAGA
-+
-IJJJJJJJJJJJCCCFFFFFHHHHHJJJJJI
- at HWI-ST960:105:D10GVACXX:2:1101:17178:2238 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGTTTGTAGTCATAATTTAGT
-+
-IJJJJJJJIJJJCBCFFFFFHHHHHJIJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:17141:2241 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCGTATGTTTCACTCTGTAACT
-+
-JJJJJJIJJJJJCCCFFDFFHHHHHJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:17119:2246 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCGAGACCAGATGTGCGATGTTT
-+
-IJJJJJJIJJJHCCCFFFFFHHHHHJJJJJIJJ
- at HWI-ST960:105:D10GVACXX:2:1101:17246:2247 1:N:0: bcd:RPI8 seq:CACACTTGAATC
-CACACTTGAATCATTTGGTTAGGTCCTTTGTTC
-+
-JJJJJJJJJJJJCCCFFFFFHHHFHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:17011:2248 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTTTTGAGGTTTTAAGATGTT
-+
-HIJJJJJJJJJJBCCFFFFFFHHHHJJIJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:17270:2162 1:N:0: bcd:RPI9 seq:CACGATCAGATC
-CACGATCAGATCCCNCTCTTTCAATGCAAATTT
-+
-IJJGJJJJJJJJCC#4ADDFHHHHHJJJJJJJJ
- at HWI-ST960:105:D10GVACXX:2:1101:17469:2169 1:N:0: bcd:RPI7 seq:CACCAGATCATC
-CACCAGATCATCTGTGTTGGTGAAGGAAGGAAC
-+
-GHI at FFG;CHIH@@+ADDDDAFHDFEG@?A?FB
diff --git a/src/libqes/test/data/test.fastq.bz2 b/src/libqes/test/data/test.fastq.bz2
deleted file mode 100644
index e79e99e..0000000
Binary files a/src/libqes/test/data/test.fastq.bz2 and /dev/null differ
diff --git a/src/libqes/test/data/test.fastq.gz b/src/libqes/test/data/test.fastq.gz
deleted file mode 100644
index a234381..0000000
Binary files a/src/libqes/test/data/test.fastq.gz and /dev/null differ
diff --git a/src/libqes/test/data/test_large.fasta.gz b/src/libqes/test/data/test_large.fasta.gz
deleted file mode 100644
index 7921c84..0000000
Binary files a/src/libqes/test/data/test_large.fasta.gz and /dev/null differ
diff --git a/src/libqes/test/data/truth/log_test.txt b/src/libqes/test/data/truth/log_test.txt
deleted file mode 100644
index 8254f87..0000000
--- a/src/libqes/test/data/truth/log_test.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-Hello World
-Hello World
diff --git a/src/libqes/test/data/truth/qes_seq_print.fa b/src/libqes/test/data/truth/qes_seq_print.fa
deleted file mode 100644
index 69029e8..0000000
--- a/src/libqes/test/data/truth/qes_seq_print.fa
+++ /dev/null
@@ -1,2 +0,0 @@
->TEST Comment 1
-AGCT
diff --git a/src/libqes/test/data/truth/qes_seq_print.fq b/src/libqes/test/data/truth/qes_seq_print.fq
deleted file mode 100644
index d93c867..0000000
--- a/src/libqes/test/data/truth/qes_seq_print.fq
+++ /dev/null
@@ -1,4 +0,0 @@
- at TEST Comment 1
-AGCT
-+
-IIII
diff --git a/src/libqes/test/helpers.c b/src/libqes/test/helpers.c
deleted file mode 100644
index 2cb8763..0000000
--- a/src/libqes/test/helpers.c
+++ /dev/null
@@ -1,207 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: helpers.c
- *
- * Description: Helpers for tests
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "helpers.h"
-
-
-/* This is how we name out output files, n_writables is the num of writable
- files we've made. */
-static int n_writables = 0;
-/* This holds the prefix. It is set (via extern) in test.c's main func. */
-char *data_prefix = NULL;
-
-
-/*=== FUNCTION ============================================================*
-Name: find_data_file
-Parameters: filepath: the file, under ./data, to find
-Description: Finds the full path to ``filepath``
-Returns: A ``char *`` on the heap that contains a valid path to the
- file ``filepath``, or NULL on error;
- *===========================================================================*/
-
-char *
-find_data_file(const char * filepath)
-{
- size_t buflen = 1<<12;
- size_t len = 0;
- char buf[buflen];
-
- /* Bail out if we can't get the data_prefix. */
- if (data_prefix == NULL) {
- return NULL;
- }
- len = snprintf(buf, buflen, "%s/data/%s", data_prefix, filepath);
- /* File name is too long, return NULL */
- if (len >= buflen) {
- return NULL;
- }
- /* Null terminate AFTER making sure len < buflen */
- buf[len] = '\0';
- /* Check we can access the file. If so, strdup & return */
- if (access(buf, F_OK) == 0) {
- char *ret = malloc(buflen + 1);
- assert(ret);
- return strncpy(ret, buf, buflen);
- }
- /* If we get to here, something's gone wrong. */
- return NULL;
-}
-
-
-/*=== FUNCTION ============================================================*
-Name: get_writable_file
-Parameters: void
-Description: Gets a temporary file which can be written to, under the data
- directory.
-Returns: A ``char *`` on the heap that contains a valid path to a file
- writable file, or NULL on error;
- *===========================================================================*/
-
-char *
-get_writable_file(void)
-{
- size_t buflen = 1<<12;
- size_t len = 0;
- char buf[buflen];
- char *ret = NULL;
-
- /* Bail out if we can't get the data_prefix. */
- if (data_prefix == NULL) {
- return NULL;
- }
- len = snprintf(buf, buflen, "%s/data/%05d", data_prefix, n_writables++);
- /* File name is too long, return NULL */
- if (len >= buflen) {
- return NULL;
- }
- /* Null terminate AFTER making sure len < buflen */
- buf[len] = '\0';
- /* Check we can access the file. If so, strdup & return */
- ret = malloc(buflen + 1);
- assert(ret);
- return strncpy(ret, buf, buflen);
-}
-
-
-/*=== FUNCTION ============================================================*
-Name: clean_writable_file
-Parameters: char *: filename
-Description: Unlink ``file`` and free the memory holding the path.
-Returns: void
- *===========================================================================*/
-
-void
-clean_writable_file(char *filepath)
-{
- if (filepath != NULL) {
- remove(filepath);
- free(filepath);
- }
-}
-
-
-/*=== FUNCTION ============================================================*
-Name: crc32_file
-Parameters: char *: filename
-Description: Calculate (using zlib) crc32 checksum.
-Returns: const char *: The crc32 sum, or NULL on error.
- *===========================================================================*/
-
-char *
-crc32_file(const char *filepath)
-{
- FILE *fp = NULL;
- size_t buflen = 1<<10;
- size_t len = 0;
- char buffer[buflen];
- uint32_t crc = 0;
- char crcbuf[9];
-
- /* Open file */
- fp = fopen(filepath, "rb");
- if (fp == NULL) {
- return NULL;
- }
- while (!feof(fp)) {
- len = fread(buffer, 1, buflen, fp);
- crc = crc32_update(crc, buffer, len);
- }
- len = snprintf(crcbuf, 9, "%08x", crc);
- crcbuf[len] = '\0';
- fclose(fp);
- return strdup(crcbuf);
-}
-
-int
-filecmp(const char *file1, const char *file2)
-{
- /* returns: -1 on error, 0 if identical, 1 if not */
- FILE *fp1 = NULL;
- FILE *fp2 = NULL;
- unsigned char *buff1 = NULL;
- unsigned char *buff2 = NULL;
- const size_t buff_size = 65535;
- int retval = 1;
-
- if (file1 == NULL || file2 == NULL) return -1;
- fp1 = fopen(file1, "r");
- fp2 = fopen(file2, "r");
- buff1 = malloc(buff_size);
- buff2 = malloc(buff_size);
- if (fp1 == NULL || fp2 == NULL || buff1 == NULL || buff2 == NULL) {
- retval = -1;
- goto exit;
- }
-
- while (!feof(fp1) && !feof(fp2)) {
- size_t bytes_read = 0;
- size_t res1 = 0;
- size_t res2 = 0;
- res1 = fread(buff1, 1, buff_size, fp1);
- res2 = fread(buff2, 1, buff_size, fp2);
- if (ferror(fp1) != 0 || ferror(fp2) != 0) {
- retval = -1;
- goto exit;
- }
- if (res1 != res2) {
- retval = 1;
- goto exit;
- }
- if (res1 == 0 && res2 == 0) {
- break;
- }
- bytes_read += res1;
- if (memcmp(buff1, buff2, res1) == 0) retval = 0;
- }
-exit:
- if (buff1 != NULL) free(buff1);
- if (fp1 != NULL) fclose(fp1);
- if (buff2 != NULL) free(buff2);
- if (fp2 != NULL) fclose(fp2);
- return retval;
-}
diff --git a/src/libqes/test/helpers.h b/src/libqes/test/helpers.h
deleted file mode 100644
index 1e9d21d..0000000
--- a/src/libqes/test/helpers.h
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: helpers.h
- *
- * Description: Helpers for tests
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#ifndef HELPERS_H
-#define HELPERS_H
-
-#include <assert.h>
-#include <stdlib.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <strings.h>
-#include <errno.h>
-#include <stdint.h>
-#include <inttypes.h>
-#include <time.h>
-#ifndef _WIN32
-# include <unistd.h>
-#endif
-
-#include <qes_libgnu.h>
-
-
-extern char *data_prefix;
-char *find_data_file(const char * filepath);
-char *get_writable_file(void);
-void clean_writable_file(char *filepath);
-char *crc32_file(const char *filepath);
-int filecmp(const char *file1, const char *file2);
-
-#endif /* HELPERS_H */
diff --git a/src/libqes/test/kseq.h b/src/libqes/test/kseq.h
deleted file mode 100644
index a5cec7c..0000000
--- a/src/libqes/test/kseq.h
+++ /dev/null
@@ -1,235 +0,0 @@
-/* The MIT License
-
- Copyright (c) 2008, 2009, 2011 Attractive Chaos <attractor at live.co.uk>
-
- Permission is hereby granted, free of charge, to any person obtaining
- a copy of this software and associated documentation files (the
- "Software"), to deal in the Software without restriction, including
- without limitation the rights to use, copy, modify, merge, publish,
- distribute, sublicense, and/or sell copies of the Software, and to
- permit persons to whom the Software is furnished to do so, subject to
- the following conditions:
-
- The above copyright notice and this permission notice shall be
- included in all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
- BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
- ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
- CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- SOFTWARE.
-*/
-
-/* Last Modified: 05MAR2012 */
-
-#ifndef AC_KSEQ_H
-#define AC_KSEQ_H
-
-#include <ctype.h>
-#include <string.h>
-#include <stdlib.h>
-
-#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
-#define KS_SEP_TAB 1 // isspace() && !' '
-#define KS_SEP_LINE 2 // line separator: "\n" (Unix) or "\r\n" (Windows)
-#define KS_SEP_MAX 2
-
-#define __KS_TYPE(type_t) \
- typedef struct __kstream_t { \
- unsigned char *buf; \
- int begin, end, is_eof; \
- type_t f; \
- } kstream_t;
-
-#define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
-#define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)
-
-#define __KS_BASIC(type_t, __bufsize) \
- static inline kstream_t *ks_init(type_t f) \
- { \
- kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t)); \
- ks->f = f; \
- ks->buf = (unsigned char*)malloc(__bufsize); \
- return ks; \
- } \
- static inline void ks_destroy(kstream_t *ks) \
- { \
- if (ks) { \
- free(ks->buf); \
- free(ks); \
- } \
- }
-
-#define __KS_GETC(__read, __bufsize) \
- static inline int ks_getc(kstream_t *ks) \
- { \
- if (ks->is_eof && ks->begin >= ks->end) return -1; \
- if (ks->begin >= ks->end) { \
- ks->begin = 0; \
- ks->end = __read(ks->f, ks->buf, __bufsize); \
- if (ks->end < __bufsize) ks->is_eof = 1; \
- if (ks->end == 0) return -1; \
- } \
- return (int)ks->buf[ks->begin++]; \
- }
-
-#ifndef KSTRING_T
-#define KSTRING_T kstring_t
-typedef struct __kstring_t {
- size_t l, m;
- char *s;
-} kstring_t;
-#endif
-
-#ifndef kroundup32
-#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
-#endif
-
-#define __KS_GETUNTIL(__read, __bufsize) \
- static int ks_getuntil2(kstream_t *ks, int delimiter, kstring_t *str, int *dret, int append) \
- { \
- if (dret) *dret = 0; \
- str->l = append? str->l : 0; \
- if (ks->begin >= ks->end && ks->is_eof) return -1; \
- for (;;) { \
- int i; \
- if (ks->begin >= ks->end) { \
- if (!ks->is_eof) { \
- ks->begin = 0; \
- ks->end = __read(ks->f, ks->buf, __bufsize); \
- if (ks->end < __bufsize) ks->is_eof = 1; \
- if (ks->end == 0) break; \
- } else break; \
- } \
- if (delimiter == KS_SEP_LINE) { \
- for (i = ks->begin; i < ks->end; ++i) \
- if (ks->buf[i] == '\n') break; \
- } else if (delimiter > KS_SEP_MAX) { \
- for (i = ks->begin; i < ks->end; ++i) \
- if (ks->buf[i] == delimiter) break; \
- } else if (delimiter == KS_SEP_SPACE) { \
- for (i = ks->begin; i < ks->end; ++i) \
- if (isspace(ks->buf[i])) break; \
- } else if (delimiter == KS_SEP_TAB) { \
- for (i = ks->begin; i < ks->end; ++i) \
- if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \
- } else i = 0; /* never come to here! */ \
- if (str->m - str->l < (size_t)(i - ks->begin + 1)) { \
- str->m = str->l + (i - ks->begin) + 1; \
- kroundup32(str->m); \
- str->s = (char*)realloc(str->s, str->m); \
- } \
- memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
- str->l = str->l + (i - ks->begin); \
- ks->begin = i + 1; \
- if (i < ks->end) { \
- if (dret) *dret = ks->buf[i]; \
- break; \
- } \
- } \
- if (str->s == 0) { \
- str->m = 1; \
- str->s = (char*)calloc(1, 1); \
- } else if (delimiter == KS_SEP_LINE && str->l > 1 && str->s[str->l-1] == '\r') --str->l; \
- str->s[str->l] = '\0'; \
- return str->l; \
- } \
- static inline int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
- { return ks_getuntil2(ks, delimiter, str, dret, 0); }
-
-#define KSTREAM_INIT(type_t, __read, __bufsize) \
- __KS_TYPE(type_t) \
- __KS_BASIC(type_t, __bufsize) \
- __KS_GETC(__read, __bufsize) \
- __KS_GETUNTIL(__read, __bufsize)
-
-#define kseq_rewind(ks) ((ks)->last_char = (ks)->f->is_eof = (ks)->f->begin = (ks)->f->end = 0)
-
-#define __KSEQ_BASIC(SCOPE, type_t) \
- SCOPE kseq_t *kseq_init(type_t fd) \
- { \
- kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t)); \
- s->f = ks_init(fd); \
- return s; \
- } \
- SCOPE void kseq_destroy(kseq_t *ks) \
- { \
- if (!ks) return; \
- free(ks->name.s); free(ks->comment.s); free(ks->seq.s); free(ks->qual.s); \
- ks_destroy(ks->f); \
- free(ks); \
- }
-
-/* Return value:
- >=0 length of the sequence (normal)
- -1 end-of-file
- -2 truncated quality string
- */
-#define __KSEQ_READ(SCOPE) \
- SCOPE int kseq_read(kseq_t *seq) \
- { \
- int c; \
- kstream_t *ks = seq->f; \
- if (seq->last_char == 0) { /* then jump to the next header line */ \
- while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@'); \
- if (c == -1) return -1; /* end of file */ \
- seq->last_char = c; \
- } /* else: the first header char has been read in the previous call */ \
- seq->comment.l = seq->seq.l = seq->qual.l = 0; /* reset all members */ \
- if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1; /* normal exit: EOF */ \
- if (c != '\n') ks_getuntil(ks, KS_SEP_LINE, &seq->comment, 0); /* read FASTA/Q comment */ \
- if (seq->seq.s == 0) { /* we can do this in the loop below, but that is slower */ \
- seq->seq.m = 256; \
- seq->seq.s = (char*)malloc(seq->seq.m); \
- } \
- while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
- if (c == '\n') continue; /* skip empty lines */ \
- seq->seq.s[seq->seq.l++] = c; /* this is safe: we always have enough space for 1 char */ \
- ks_getuntil2(ks, KS_SEP_LINE, &seq->seq, 0, 1); /* read the rest of the line */ \
- } \
- if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */ \
- if (seq->seq.l + 1 >= seq->seq.m) { /* seq->seq.s[seq->seq.l] below may be out of boundary */ \
- seq->seq.m = seq->seq.l + 2; \
- kroundup32(seq->seq.m); /* rounded to the next closest 2^k */ \
- seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
- } \
- seq->seq.s[seq->seq.l] = 0; /* null terminated string */ \
- if (c != '+') return seq->seq.l; /* FASTA */ \
- if (seq->qual.m < seq->seq.m) { /* allocate memory for qual in case insufficient */ \
- seq->qual.m = seq->seq.m; \
- seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m); \
- } \
- while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
- if (c == -1) return -2; /* error: no quality string */ \
- while (ks_getuntil2(ks, KS_SEP_LINE, &seq->qual, 0, 1) >= 0 && seq->qual.l < seq->seq.l); \
- seq->last_char = 0; /* we have not come to the next header line */ \
- if (seq->seq.l != seq->qual.l) return -2; /* error: qual string is of a different length */ \
- return seq->seq.l; \
- }
-
-#define __KSEQ_TYPE(type_t) \
- typedef struct { \
- kstring_t name, comment, seq, qual; \
- int last_char; \
- kstream_t *f; \
- } kseq_t;
-
-#define KSEQ_INIT2(SCOPE, type_t, __read) \
- KSTREAM_INIT(type_t, __read, 16384) \
- __KSEQ_TYPE(type_t) \
- __KSEQ_BASIC(SCOPE, type_t) \
- __KSEQ_READ(SCOPE)
-
-#define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
-
-#define KSEQ_DECLARE(type_t) \
- __KS_TYPE(type_t) \
- __KSEQ_TYPE(type_t) \
- extern kseq_t *kseq_init(type_t fd); \
- void kseq_destroy(kseq_t *ks); \
- int kseq_read(kseq_t *seq);
-
-#endif
diff --git a/src/libqes/test/kseqcat.c b/src/libqes/test/kseqcat.c
deleted file mode 100644
index f6d38ce..0000000
--- a/src/libqes/test/kseqcat.c
+++ /dev/null
@@ -1,41 +0,0 @@
-#include "qes_config.h"
-#include <stdio.h>
-#include <stdlib.h>
-
-#include <zlib.h>
-
-#include "kseq.h"
-
-#ifdef ZLIB_FOUND
-# include <zlib.h>
- KSEQ_INIT(gzFile, gzread)
-#else
-# include <sys/stat.h>
-# include <fcntl.h>
- KSEQ_INIT(int, read)
-#endif
-
-int main(int argc, char *argv[])
-{
- if (argc < 2) return 1;
- const char *fname = argv[1];
- gzFile fp = gzopen(fname, "r");
- kseq_t *kseq = kseq_init(fp);
- ssize_t res = 0;
- while((res = kseq_read(kseq)) > 0) {
- if (kseq->qual.l < 1) {
- // fasta
- printf(">%s %s\n", kseq->name.s, kseq->comment.s);
- puts(kseq->seq.s);
- } else {
- // fastq
- printf("@%s %s\n", kseq->name.s, kseq->comment.s);
- puts(kseq->seq.s);
- puts("+");
- puts(kseq->qual.s);
- }
- }
- kseq_destroy(kseq);
- gzclose(fp);
- return 0;
-}
diff --git a/src/libqes/test/logdemo.c b/src/libqes/test/logdemo.c
deleted file mode 100644
index b408ced..0000000
--- a/src/libqes/test/logdemo.c
+++ /dev/null
@@ -1,50 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: logdemo.c
- * Description: Demontrate libqes logging
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include <qes_log.h>
-
-int
-main (int argc, char *argv[])
-{
- struct qes_logger *logger = qes_logger_create();
-
- (void) argc;
- (void) argv;
-
- qes_logger_init(logger, "Test Logger", QES_LOG_DEBUG);
- qes_logger_add_destination_formatted(logger, stdout, QES_LOG_DEBUG,
- &qes_log_formatter_pretty);
-
- qes_log_message_debug(logger, "Debug message, nice and quiet\n");
- qes_log_message_info(logger, "Informative message, clearer\n");
- qes_log_message_warning(logger, "Warning message, pay attention!\n");
- qes_log_message_error(logger, "Error message, something's gone wrong\n");
- qes_log_message_fatal(logger, "Fatal message, I'm leaving now\n");
-
- qes_logger_destroy(logger);
- return EXIT_SUCCESS;
-}
diff --git a/src/libqes/test/qes_seqcat.c b/src/libqes/test/qes_seqcat.c
deleted file mode 100644
index 4b1aade..0000000
--- a/src/libqes/test/qes_seqcat.c
+++ /dev/null
@@ -1,30 +0,0 @@
-#include "qes_config.h"
-#include <stdio.h>
-#include <stdlib.h>
-
-#include <qes_seqfile.h>
-
-int main(int argc, char *argv[])
-{
- if (argc < 2) return 1;
- const char *fname = argv[1];
- struct qes_seq *seq = qes_seq_create();
- struct qes_seqfile *sf = qes_seqfile_create(fname, "r");
- ssize_t res = 0;
- while((res = qes_seqfile_read(sf, seq)) > 0) {
- if (seq->qual.len < 1) {
- // fasta
- printf(">%s %s\n", seq->name.str, seq->comment.str);
- puts(seq->seq.str);
- } else {
- // fastq
- printf("@%s %s\n", seq->name.str, seq->comment.str);
- puts(seq->seq.str);
- puts("+");
- puts(seq->qual.str);
- }
- }
- qes_seqfile_destroy(sf);
- qes_seq_destroy(seq);
- return 0;
-}
diff --git a/src/libqes/test/qes_seqprint.c b/src/libqes/test/qes_seqprint.c
deleted file mode 100644
index 773550c..0000000
--- a/src/libqes/test/qes_seqprint.c
+++ /dev/null
@@ -1,21 +0,0 @@
-#include "qes_config.h"
-#include <stdio.h>
-#include <stdlib.h>
-
-#include <qes_seqfile.h>
-
-int main(int argc, char *argv[])
-{
- if (argc < 2) return 1;
- const char *fname = argv[1];
- struct qes_seq *seq = qes_seq_create();
- struct qes_seqfile *sf = qes_seqfile_create(fname, "r");
- ssize_t res = 0;
- while((res = qes_seqfile_read(sf, seq)) > 0) {
- int fasta = seq->qual.len < 1;
- qes_seq_print(seq, stdout, fasta, 0);
- }
- qes_seqfile_destroy(sf);
- qes_seq_destroy(seq);
- return 0;
-}
diff --git a/src/libqes/test/test.c b/src/libqes/test/test.c
deleted file mode 100644
index c3e1a3c..0000000
--- a/src/libqes/test/test.c
+++ /dev/null
@@ -1,80 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: test.c
- *
- * Description: Tests for libqes
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "tests.h"
-
-
-struct testgroup_t libqes_tests[] = {
- {"qes/util/", qes_util_tests},
- {"qes/match/", qes_match_tests},
- {"qes/file/", qes_file_tests},
- {"qes/seqfile/", qes_seqfile_tests},
- {"qes/seq/", qes_seq_tests},
- {"qes/log/", qes_log_tests},
- {"qes/sequtil/", qes_sequtil_tests},
- {"testdata/", data_tests},
- {"testhelpers/", helper_tests},
- END_OF_GROUPS
-};
-
-
-/*
- * === FUNCTION =============================================================
- * Name: main
- * Description: Run all tests
- * ============================================================================
- */
-
-int
-main (int argc, const char *argv[])
-{
- int res;
- int our_argc = argc;
- const char **our_argv = argv;
-
- data_prefix = NULL;
- if (argc>1) {
- data_prefix = strdup(argv[1]);
- our_argc -= 1;
- our_argv += 1;
- }
- if (data_prefix == NULL) {
- data_prefix = strdup(".");
- assert(data_prefix != NULL);
- }
- if (access(data_prefix, W_OK | X_OK | R_OK) != 0) {
- fprintf(stderr, "ERROR: Could not access data prefix dir '%s'\n",
- data_prefix);
- fprintf(stderr, "Usage: test_libqes <DATA_DIR> [<test>]\n");
- free(data_prefix);
- exit(EXIT_FAILURE);
- }
- res = tinytest_main(our_argc, our_argv, libqes_tests);
- free(data_prefix);
- return res;
-}
diff --git a/src/libqes/test/test_file.c b/src/libqes/test/test_file.c
deleted file mode 100644
index 97c604c..0000000
--- a/src/libqes/test/test_file.c
+++ /dev/null
@@ -1,446 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: test_file.c
- *
- * Description: Test qes_file
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "tests.h"
-#include <qes_file.h>
-
-
-static void
-test_qes_file_open (void *ptr)
-{
- struct qes_file *file = NULL;
- struct qes_file *badfile = NULL;
- char *fname = NULL;
-
- (void) ptr;
- /* Test file opening for reading */
- fname = find_data_file("loremipsum.txt");
- tt_assert(fname != NULL);
- file = qes_file_open(fname, "r");
- tt_ptr_op(file, !=, NULL);
- tt_int_op(file->mode, ==, QES_FILE_MODE_READ);
- qes_file_close(file);
- free(fname);
- /* test zipped file opening for reading */
- fname = find_data_file("loremipsum.txt.gz");
- tt_assert(fname != NULL);
- file = qes_file_open(fname, "r");
- tt_ptr_op(file, !=, NULL);
- tt_int_op(file->mode, ==, QES_FILE_MODE_READ);
- qes_file_close(file);
- free(fname);
- /* read with non-existant file */
- fname = get_writable_file();
- tt_assert(fname != NULL);
- file = qes_file_open(fname, "r");
- tt_ptr_op(file, ==, NULL);
- clean_writable_file(fname);
- fname = NULL;
- /* writing with gziped file */
- fname = get_writable_file();
- tt_assert(fname != NULL);
- file = qes_file_open(fname, "w");
- tt_ptr_op(file, !=, NULL);
- tt_int_op(file->mode, ==, QES_FILE_MODE_WRITE);
- clean_writable_file(fname);
- fname = NULL;
- /* With non-existant file path */
- badfile = qes_file_open("non/existent.file", "w");
- tt_ptr_op(badfile, ==, NULL);
-
-end:
- qes_file_close(file);
- qes_file_close(badfile);
- if (fname != NULL) free(fname);
-}
-
-static void
-test_qes_file_close (void *ptr)
-{
- struct qes_file *file = NULL;
- struct qes_file *nullfile = NULL;
- char *fname = NULL;
-
- (void) ptr;
- /* Open file */
- fname = find_data_file("loremipsum.txt");
- tt_assert(fname != NULL);
- file = qes_file_open(fname, "r");
- tt_assert(file);
- qes_file_close(file);
- tt_ptr_op(file, ==, NULL);
- /* check with null poitner, ensure no problems are caused. */
- qes_file_close(nullfile);
- tt_ptr_op(nullfile, ==, NULL);
-end:
- qes_file_close(file);
- free(fname);
-}
-
-
-static void
-test_qes_file_rewind (void *ptr)
-{
- struct qes_file *file = NULL;
- size_t bufsize = 1<<10;
- char buffer[bufsize];
- ssize_t res = 0;
- char *fname = NULL;
-
- (void) ptr;
- /* Open file */
- fname = find_data_file("loremipsum.txt");
- tt_assert(fname != NULL);
- file = qes_file_open(fname, "r");
- tt_assert(file);
- while (res != EOF) {
- res = qes_file_readline(file, buffer, bufsize);
- }
- tt_int_op(file->filepos, ==, loremipsum_fsize);
- tt_int_op(QES_ZTELL(file->fp), ==, loremipsum_fsize);
- tt_assert(file->eof);
- tt_assert(file->feof);
- qes_file_rewind(file);
- tt_int_op(file->filepos, ==, 0);
- tt_assert(!file->eof);
- tt_assert(!file->feof);
- tt_int_op(QES_ZTELL(file->fp), ==, 0);
-end:
- qes_file_close(file);
- free(fname);
-}
-
-static void
-test_qes_file_readline (void *ptr)
-{
- struct qes_file *file = NULL;
- size_t bufsize = 1<<10;
- char buffer[bufsize];
- ssize_t res_len = 0;
- off_t orig_filepos = 0;
- size_t iii;
- char *fname = NULL;
-
- (void) ptr;
- /* Open file */
- fname = find_data_file("loremipsum.txt");
- tt_assert(fname != NULL);
- file = qes_file_open(fname, "r");
- /* Check each line is of the right length, that the length is returned,
- * that the string is as expected, and that file->filepos is updated.
- */
- for (iii = 0; iii < n_loremipsum_lines; iii++) {
- orig_filepos = file->filepos;
- res_len = qes_file_readline(file, buffer, bufsize);
- tt_int_op(res_len, ==, strlen(buffer));
- tt_int_op(res_len, ==, loremipsum_line_lens[iii]);
- tt_str_op(buffer, ==, loremipsum_lines[iii]);
- tt_int_op(file->filepos - orig_filepos, ==, loremipsum_line_lens[iii]);
- }
- /* Check that a file at EOF returns EOF. */
- tt_int_op(file->filepos, ==, loremipsum_fsize);
- tt_int_op(qes_file_readline(file, buffer, bufsize), ==, EOF);
- tt_assert(file->eof)
- /* Test with bad parameters */
- tt_int_op(qes_file_readline(NULL, buffer, bufsize), ==, -2);
- tt_int_op(qes_file_readline(file, NULL, bufsize), ==, -2);
- tt_int_op(qes_file_readline(file, buffer, 0), ==, -2);
-
-end:
- qes_file_close(file);
- free(fname);
-}
-
-static void
-test_qes_file_getuntil (void *ptr)
-{
- struct qes_file *file = NULL;
- const size_t bufsize = 1<<10;
- char buffer[bufsize];
- ssize_t res_len = 0;
- size_t expt_len = 0;
- off_t orig_filepos = 0;
- off_t our_filepos = 0;
- size_t iii;
- const size_t n_delims = 5;
- const int delims[] = {' ', ',', '.', '\n', '\n'};
- const char *delim_words[] = {
- "Lorem ",
- "ipsum dolor sit amet,",
- " consectetur adipiscing elit.",
- " Donec ornare tortor et\n",
- "rhoncus iaculis. Sed suscipit, arcu nec elementum vestibulum, tortor tortor\n",
- };
- char *fname = NULL;
-
- (void) ptr;
- /* Open file */
- fname = find_data_file("loremipsum.txt");
- tt_assert(fname != NULL);
- file = qes_file_open(fname, "r");
- /* Check each token is of the right length, that the length is returned,
- * that the string is as expected, and that file->filepos is updated.
- */
- for (iii = 0; iii < n_delims; iii++) {
- orig_filepos = file->filepos;
- res_len = qes_file_getuntil(file, delims[iii], buffer, bufsize);
- our_filepos += res_len;
- expt_len = strnlen(delim_words[iii], bufsize);
- tt_int_op(res_len, ==, strnlen(buffer, bufsize));
- tt_int_op(res_len, ==, expt_len);
- tt_str_op(buffer, ==, delim_words[iii]);
- tt_int_op(file->filepos - orig_filepos, ==, expt_len);
- tt_int_op(file->filepos, ==, our_filepos);
- }
- /* Check we can give EOF as the char and make it give us the remainder of
- the file */
- orig_filepos = file->filepos;
- res_len = qes_file_getuntil(file, EOF, buffer, bufsize);
- expt_len = loremipsum_fsize - our_filepos;
- our_filepos += res_len;
- tt_int_op(res_len, ==, strnlen(buffer, bufsize));
- tt_int_op(res_len, ==, expt_len);
- tt_int_op(file->filepos - orig_filepos, ==, expt_len);
- tt_int_op(file->filepos, ==, our_filepos);
- tt_assert(file->eof)
- tt_int_op(file->filepos, ==, loremipsum_fsize);
- /* Check that a file at EOF returns EOF. */
- tt_int_op(file->filepos, ==, loremipsum_fsize);
- tt_int_op(qes_file_getuntil(file, '\n', buffer, bufsize), ==, EOF);
- tt_assert(file->eof)
- /* Test with bad parameters */
- QES_ZREWIND(file->fp);
- file->eof = 0;
- file->filepos = 0;
- tt_int_op(qes_file_getuntil(NULL, '\n', buffer, bufsize), ==, -2);
- tt_int_op(qes_file_getuntil(file, 256, buffer, bufsize), ==, -2);
- tt_int_op(qes_file_getuntil(file, '\n', NULL, bufsize), ==, -2);
- tt_int_op(qes_file_getuntil(file, '\n', buffer, 0), ==, -2);
-end:
- qes_file_close(file);
- if (fname != NULL) free(fname);
-}
-
-static void
-test_qes_file_peek (void *ptr)
-{
- int res = 0;
- struct qes_file *file = NULL;
- off_t orig_filepos = 0;
- char *fname = NULL;
-
- (void) ptr;
- /* Open file and save pos */
- fname = find_data_file("loremipsum.txt");
- tt_assert(fname != NULL);
- file = qes_file_open(fname, "r");
- orig_filepos = file->filepos;
- /* Peek a char */
- res = qes_file_peek(file);
- /* Check it's the right char */
- tt_int_op(res, ==, loremipsum_lines[0][0]);
- /* And that the filepos hasn't changed */
- tt_int_op(file->filepos , ==, orig_filepos);
- /* And that the same char is returned again */
- res = qes_file_peek(file);
- tt_int_op(res, ==, loremipsum_lines[0][0]);
- /* And that it returns an error on being given a null pointer */
- tt_int_op(qes_file_peek(NULL), ==, -2);
-end:
- qes_file_close(file);
- if (fname != NULL) free(fname);
-}
-
-static void
-test_qes_file_guess_mode (void *ptr)
-{
- const char *modes[] = {
- "r", "rb", "rb8", "rT", "rbT",
- "w", "wb", "wb8", "wT", "wbT",
- "a", "ab", "ab8", "aT", "abT",
- "+", "+b", "+b8", "+T", "+bT",
- };
- const int mode_results[] = {
- QES_FILE_MODE_READ, QES_FILE_MODE_READ, QES_FILE_MODE_READ,
- QES_FILE_MODE_READ, QES_FILE_MODE_READ, QES_FILE_MODE_WRITE,
- QES_FILE_MODE_WRITE, QES_FILE_MODE_WRITE, QES_FILE_MODE_WRITE,
- QES_FILE_MODE_WRITE, QES_FILE_MODE_WRITE, QES_FILE_MODE_WRITE,
- QES_FILE_MODE_WRITE, QES_FILE_MODE_WRITE, QES_FILE_MODE_WRITE,
- QES_FILE_MODE_UNKNOWN, QES_FILE_MODE_UNKNOWN, QES_FILE_MODE_UNKNOWN,
- QES_FILE_MODE_UNKNOWN, QES_FILE_MODE_UNKNOWN,
- };
- const size_t num_modes = 20;
- size_t iii;
- (void) ptr;
- for (iii = 0; iii < num_modes; iii++) {
- tt_int_op(qes_file_guess_mode(modes[iii]), ==, mode_results[iii]);
- }
-end:
- ;
-}
-
-static void
-test_qes_file_readline_realloc (void *ptr)
-{
- char *buf = NULL;
- char *smallbuf = NULL;
- const size_t smallbuf_len = 4;
- const size_t buf_len = 1<<10; /* 1024b */
- struct qes_file *file = NULL;
- ssize_t ret = 0;
- off_t fpos = 0;
- size_t line_num;
- char *nulcp = NULL;
- size_t tmpsz = buf_len;
- char *fname = NULL;
-
- (void) ptr;
- /* Open file and save pos */
- fname = find_data_file("loremipsum.txt");
- /* This should always work, so long as you run it from the right dir */
- file = qes_file_open(fname, "r");
- buf = calloc(buf_len, sizeof(*buf));
- smallbuf = calloc(smallbuf_len, sizeof(*smallbuf));
- tt_assert(file && buf && smallbuf);
- /* Check each line is of the right length, that the length is returned,
- * that the string is as expected, and that file->filepos is updated.
- */
- for (line_num = 0; line_num < n_loremipsum_lines; line_num++) {
- ret = qes_file_readline_realloc(file, &buf, &tmpsz);
- fpos += ret;
- tt_int_op(fpos, ==, file->filepos);
- tt_str_op(buf, ==, loremipsum_lines[line_num]);
- tt_int_op(strlen(buf), ==, loremipsum_line_lens[line_num]);
- tt_int_op(ret, ==, loremipsum_line_lens[line_num]);
- tt_int_op(buf[ret], ==, '\0');
- tt_int_op(tmpsz, ==, buf_len);
- tt_int_op(tmpsz, >=, qes_roundupz(loremipsum_line_lens[line_num]));
- }
- tt_int_op(file->filepos, ==, loremipsum_fsize);
- ret = qes_file_readline_realloc(file, &buf, &tmpsz);
- tt_assert(file->eof);
- tt_int_op(ret, ==, EOF);
- qes_file_close(file);
- /*
- * Test w/ small buffer
- */
- /* Do the same checks, but with a buffer that needs resizing */
- file = qes_file_open(fname, "r");
- tmpsz = smallbuf_len;
- fpos = 0;
- for (line_num = 0; line_num < n_loremipsum_lines; line_num++) {
- ret = qes_file_readline_realloc(file, &smallbuf, &tmpsz);
- fpos += ret;
- tt_int_op(fpos, ==, file->filepos);
- tt_str_op(smallbuf, ==, loremipsum_lines[line_num]);
- tt_int_op(strlen(smallbuf), ==, loremipsum_line_lens[line_num]);
- tt_int_op(ret, ==, loremipsum_line_lens[line_num]);
- tt_int_op(tmpsz, !=, smallbuf_len);
- tt_int_op(tmpsz, >=, qes_roundupz(loremipsum_line_lens[line_num]));
- tt_int_op(smallbuf[ret], ==, '\0');
- }
- tt_int_op(file->filepos, ==, loremipsum_fsize);
- /* Test with EOF file */
- tmpsz = buf_len;
- ret = qes_file_readline_realloc(file, &buf, &tmpsz);
- tt_int_op(ret, ==, EOF);
- tt_str_op(buf, ==, "");
- tt_int_op(strlen(buf), ==, 0);
- tt_int_op(tmpsz, ==, buf_len);
- tt_assert(file->eof)
- qes_file_close(file);
- /*
- * Test bad things
- */
- /* Null buf. Should alloc a buffer and fill it */
- file = qes_file_open(fname, "r");
- line_num = 0;
- ret = qes_file_readline_realloc(file, &nulcp, &tmpsz);
- tt_int_op(ret, ==, loremipsum_line_lens[line_num]);
- tt_str_op(nulcp, ==, loremipsum_lines[line_num]);
- tt_int_op(strlen(nulcp), ==, loremipsum_line_lens[line_num]);
- tt_int_op(tmpsz, ==, __INIT_LINE_LEN);
- /* Null file */
- ret = qes_file_readline_realloc(NULL, &buf, &tmpsz);
- tt_int_op(ret, ==, -2);
- /* This shouldn't change and is set in the prev. test */
- tt_int_op(tmpsz, ==, __INIT_LINE_LEN);
- /* Both buf & file null */
- ret = qes_file_readline_realloc(NULL, &nulcp, &tmpsz);
- tt_int_op(ret, ==, -2);
- tt_int_op(tmpsz, ==, __INIT_LINE_LEN);
-end:
- if (buf != NULL) free(buf);
- if (smallbuf != NULL) free(smallbuf);
- if (nulcp != NULL) free(nulcp);
- if (file != NULL) qes_file_close(file);
- free(fname);
-}
-
-static void
-test_qes_file_ok (void *ptr)
-{
- struct qes_file *file;
- char *writeable = NULL;
- char *readable = NULL;
-
- (void) ptr;
- readable = find_data_file("loremipsum.txt");
- writeable = get_writable_file();
- /* Should result in an OK file */
- file = qes_file_open(readable, "r");
- tt_assert(qes_file_ok(file));
- tt_assert(qes_file_readable(file));
- qes_file_close(file);
- file = qes_file_open("nosuchfile", "r");
- tt_assert(!qes_file_ok(file));
- tt_assert(!qes_file_readable(file));
- qes_file_close(file);
- file = qes_file_open(writeable, "w");
- tt_assert(qes_file_ok(file));
- tt_assert(!qes_file_readable(file));
- qes_file_close(file);
-end:
- if (file != NULL) qes_file_close(file);
- clean_writable_file(writeable);
- free(readable);
-
-}
-
-struct testcase_t qes_file_tests[] = {
- { "qes_file_open", test_qes_file_open, 0, NULL, NULL},
- { "qes_file_peek", test_qes_file_peek, 0, NULL, NULL},
- { "qes_file_readline", test_qes_file_readline, 0, NULL, NULL},
- { "qes_file_readline_realloc", test_qes_file_readline_realloc, 0, NULL, NULL},
- { "qes_file_guess_mode", test_qes_file_guess_mode, 0, NULL, NULL},
- { "qes_file_close", test_qes_file_close, 0, NULL, NULL},
- { "qes_file_rewind", test_qes_file_rewind, 0, NULL, NULL},
- { "qes_file_getuntil", test_qes_file_getuntil, 0, NULL, NULL},
- { "qes_file_ok", test_qes_file_ok, 0, NULL, NULL},
- END_OF_TESTCASES
-};
diff --git a/src/libqes/test/test_helpers.c b/src/libqes/test/test_helpers.c
deleted file mode 100644
index f82b1a7..0000000
--- a/src/libqes/test/test_helpers.c
+++ /dev/null
@@ -1,70 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: test_helpers.c
- *
- * Description: Tests of test/helpers.c
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "tests.h"
-
-
-static void
-test_crc32_file(void *data)
-{
- char *crc = NULL;
- char *fname = NULL;
-
- (void) data;
- fname = find_data_file("loremipsum.txt");
- crc = crc32_file(fname);
- tt_str_op(crc, ==, "9f20f7ec");
-end:
- free(fname);
- free(crc);
-}
-
-static void
-test_filecmp(void *data)
-{
- char *fname1 = NULL;
- char *fname2 = NULL;
-
- (void) data;
- fname1 = find_data_file("loremipsum.txt");
- fname2 = find_data_file("loremipsum.txt.gz");
- tt_int_op(filecmp(fname1, fname1), ==, 0);
- tt_int_op(filecmp(fname1, fname2), ==, 1);
- tt_int_op(filecmp(NULL, fname2), ==, -1);
- tt_int_op(filecmp("/does/not/exist/", fname2), ==, -1);
-
-end:
- free(fname1);
- free(fname2);
-}
-
-struct testcase_t helper_tests[] = {
- { "crc32_file", test_crc32_file, 0, NULL, NULL},
- { "filecmp", test_filecmp, 0, NULL, NULL},
- END_OF_TESTCASES
-};
diff --git a/src/libqes/test/test_log.c b/src/libqes/test/test_log.c
deleted file mode 100644
index d4cfc96..0000000
--- a/src/libqes/test/test_log.c
+++ /dev/null
@@ -1,189 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: test_log.c
- *
- * Description: Test logging
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "tests.h"
-#include <qes_util.h>
-#include <qes_log.h>
-
-
-static void
-test_qes_logger_setup(void *ptr)
-{
- int res = 0;
- struct qes_logger *logger = NULL;
-
- (void) ptr;
- /* Test that when created, the logger has logical initial values */
- logger = qes_logger_create();
- tt_ptr_op(logger, !=, NULL);
- tt_ptr_op(logger->destinations, ==, NULL);
- tt_ptr_op(logger->name, ==, NULL);
- tt_int_op(logger->n_destinations, ==, 0);
- tt_int_op(logger->level, ==, QES_LOG_DEBUG);
- tt_int_op(logger->lock, ==, 0);
-
- /* Add a destination, check it is there */
- res = qes_logger_add_destination(logger, stderr, QES_LOG_ERROR);
- tt_int_op(res, ==, 0);
- tt_ptr_op(logger->destinations, !=, NULL);
- tt_ptr_op(logger->destinations[0].stream, ==, stderr);
- tt_int_op(logger->destinations[0].level, ==, QES_LOG_ERROR);
- tt_int_op(logger->n_destinations, ==, 1);
- qes_logger_destroy(logger);
- tt_ptr_op(logger, ==, NULL);
-
-end:
- if (logger != NULL) {
- if (logger->destinations != NULL) free(logger->destinations);
- if (logger->name != NULL) free(logger->name);
- free(logger);
- }
-}
-
-
-static void
-test_qes_logger_init(void *ptr)
-{
- int res = 0;
- struct qes_logger *logger = NULL;
-
- (void) ptr;
- logger = qes_logger_create();
- tt_ptr_op(logger, !=, NULL);
-
- /* Test the init function sets values correctly */
- res = qes_logger_init(logger, "test logger", QES_LOG_INFO);
- tt_int_op(res, ==, 0);
- tt_ptr_op(logger->name, !=, NULL);
- tt_int_op(logger->level, ==, QES_LOG_INFO);
- tt_int_op(logger->lock, ==, 0);
-
- /* test that we error out if we give init NULL */
- res = qes_logger_init(NULL, "test logger", QES_LOG_INFO);
- tt_int_op(res, ==, 1);
-
- /* Test that we silently set logger->name to NULL if we pass NULL */
- res = qes_logger_init(logger, NULL, QES_LOG_INFO);
- tt_int_op(res, ==, 0);
- tt_ptr_op(logger->name, ==, NULL);
-
-end:
- if (logger != NULL) {
- if (logger->destinations != NULL) free(logger->destinations);
- if (logger->name != NULL) free(logger->name);
- free(logger);
- }
-}
-
-static void
-test_qes_logger_logging(void *ptr)
-{
- int res = 0;
- struct qes_logger *logger = NULL;
- char *log_fname = NULL;
- char *truth_fname = NULL;
- FILE *log_file = NULL;
-
- (void) ptr;
- /* Set up a logger, with an actual file as output */
- logger = qes_logger_create();
- tt_ptr_op(logger, !=, NULL);
- truth_fname = find_data_file("truth/log_test.txt");
- tt_ptr_op(truth_fname, !=, NULL);
- log_fname = get_writable_file();
- tt_ptr_op(log_fname, !=, NULL);
- log_file = fopen(log_fname, "w");
- tt_ptr_op(log_file, !=, NULL);
- res = qes_logger_add_destination(logger, log_file, QES_LOG_INFO);
- tt_int_op(res, ==, 0);
-
- /* Test printing to the file using the message functions */
- qes_log_message_debug(logger, "Hello World\n"); /* wont' print */
- qes_log_message_info(logger, "Hello World\n"); /* should print */
-
- /* Test printing to the file with the format functions */
- qes_log_format_debug(logger, "%s\n", "Hello World");
- qes_log_format_info(logger, "%s\n", "Hello World");
-
- /* Test the output file was created correctly */
- tt_int_op(filecmp(log_fname, truth_fname), ==, 0);
-
-end:
- if (log_file != NULL) fclose(log_file);
- if (truth_fname != NULL) free(truth_fname);
- if (log_fname != NULL) free(log_fname);
- qes_logger_destroy(logger);
-}
-
-static void
-test_qes_log_entry(void *ptr)
-{
- int res = 0;
- struct qes_log_entry *entry = NULL;
-
- (void) ptr;
- /* Test that create gives us a valid entry with sane defaults */
- entry = qes_log_entry_create();
- tt_ptr_op(entry, !=, NULL);
- tt_ptr_op(entry->message, ==, NULL);
- tt_int_op(entry->level, ==, QES_LOG_DEBUG);
-
- /* Check that init fills the entry appropriately */
- res = qes_log_entry_init(entry, QES_LOG_ERROR, "Test");
- tt_int_op(res, ==, 0);
- tt_ptr_op(entry, !=, NULL);
- tt_str_op(entry->message, ==, "Test");
- tt_int_op(entry->level, ==, QES_LOG_ERROR);
-
- /* test that clear clears an entry, without freeing the entry itself */
- qes_log_entry_clear(entry);
- tt_ptr_op(entry, !=, NULL);
- tt_ptr_op(entry->message, ==, NULL);
- tt_int_op(entry->level, ==, QES_LOG_DEBUG);
-
- /* test formatting an entry */
- res = qes_log_entry_format(entry, QES_LOG_ERROR, "%s", "Test");
- tt_int_op(res, ==, 0);
- tt_ptr_op(entry, !=, NULL);
- tt_str_op(entry->message, ==, "Test");
- tt_int_op(entry->level, ==, QES_LOG_ERROR);
-
- qes_log_entry_destroy(entry);
- tt_ptr_op(entry, ==, NULL);
-
-end:
- qes_log_entry_destroy(entry);
-}
-
-struct testcase_t qes_log_tests[] = {
- { "qes_logger_setup", test_qes_logger_setup, 0, NULL, NULL},
- { "qes_logger_init", test_qes_logger_init, 0, NULL, NULL},
- { "qes_logger_logging", test_qes_logger_logging, 0, NULL, NULL},
- { "qes_log_entry", test_qes_log_entry, 0, NULL, NULL},
- END_OF_TESTCASES
-};
diff --git a/src/libqes/test/test_match.c b/src/libqes/test/test_match.c
deleted file mode 100644
index 3ee0966..0000000
--- a/src/libqes/test/test_match.c
+++ /dev/null
@@ -1,105 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: test_match.c
- *
- * Description: Test qes_match functions
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "tests.h"
-#include <qes_match.h>
-#include <limits.h>
-
-
-static void
-test_qes_hamming (void *p)
-{
- (void) (p);
- /* Simple stuff */
- tt_int_op(qes_match_hamming("ACTTG", "ACTTG", 5), ==, 0);
- tt_int_op(qes_match_hamming("ACTTG", "ACTGG", 5), ==, 1);
- /* Different lengths */
- tt_int_op(qes_match_hamming("ACTTGA", "ACTTG", 5), ==, 0);
- tt_int_op(qes_match_hamming("ACTTG", "ACTTGA", 5), ==, 0);
- tt_int_op(qes_match_hamming("ACTTG", "ACTGGA", 5), ==, 1);
- tt_int_op(qes_match_hamming("ACTTG", "ACTGGA", 6), ==, 2);
- tt_int_op(qes_match_hamming("ACTTG", "ACTTGA", 6), ==, 1);
- /* Make it guess lengths */
- tt_int_op(qes_match_hamming("ACTTG", "ACTTG", 0), ==, 0);
- tt_int_op(qes_match_hamming("ACATG", "ACTTG", 0), ==, 1);
- tt_int_op(qes_match_hamming("ACTTG", "ACTTGT", 0), ==, 0);
- tt_int_op(qes_match_hamming("ACATG", "ACTTGT", 0), ==, 1);
- tt_int_op(qes_match_hamming("ACTTGT", "ACTTG", 0), ==, 0);
- /* Give it hell */
- tt_int_op(qes_match_hamming("ACTTG", NULL, 0), ==, -1);
- tt_int_op(qes_match_hamming(NULL, "ACTTG", 0), ==, -1);
- tt_int_op(qes_match_hamming(NULL, NULL, 0), ==, -1);
-end:
- ;
-}
-
-
-static void
-test_qes_hamming_max (void *p)
-{
-
- (void) (p);
- /* Same tests as per hamming, max is INT_MAX */
- /* Simple stuff */
- tt_int_op(qes_match_hamming_max("ACTTG", "ACTTG", 5, INT_MAX), ==, 0);
- tt_int_op(qes_match_hamming_max("ACTTG", "ACTGG", 5, INT_MAX), ==, 1);
- /* Different lengths */
- tt_int_op(qes_match_hamming_max("ACTTGA", "ACTTG", 5, INT_MAX), ==, 0);
- tt_int_op(qes_match_hamming_max("ACTTG", "ACTTGA", 5, INT_MAX), ==, 0);
- tt_int_op(qes_match_hamming_max("ACTTG", "ACTGGA", 5, INT_MAX), ==, 1);
- tt_int_op(qes_match_hamming_max("ACTTG", "ACTGGA", 6, INT_MAX), ==, 2);
- tt_int_op(qes_match_hamming_max("ACTTG", "ACTTGA", 6, INT_MAX), ==, 1);
- /* Make it guess lengths */
- tt_int_op(qes_match_hamming_max("ACTTG", "ACTTG", 0, INT_MAX), ==, 0);
- tt_int_op(qes_match_hamming_max("ACATG", "ACTTG", 0, INT_MAX), ==, 1);
- tt_int_op(qes_match_hamming_max("ACTTG", "ACTTGT", 0, INT_MAX), ==, 0);
- tt_int_op(qes_match_hamming_max("ACATG", "ACTTGT", 0, INT_MAX), ==, 1);
- tt_int_op(qes_match_hamming_max("ACTTGT", "ACTTG", 0, INT_MAX), ==, 0);
- /* Test it bails out when over ``max`` */
- tt_int_op(qes_match_hamming_max("ACTTG", "ACTGG", 5, 1), ==, 1);
- tt_int_op(qes_match_hamming_max("ACTTG", "ACTGG", 5, 0), ==, 1);
- tt_int_op(qes_match_hamming_max("ACTTG", "ACTGA", 5, 0), ==, 1);
- tt_int_op(qes_match_hamming_max("ACTTG", "ACTGA", 5, 1), ==, 2);
- tt_int_op(qes_match_hamming_max("ACTTG", "ACTGA", 5, 2), ==, 2);
- /* Give it hell */
- tt_int_op(qes_match_hamming_max("ACTTG", NULL, 0, INT_MAX), ==, -1);
- tt_int_op(qes_match_hamming_max(NULL, "ACTTG", 0, INT_MAX), ==, -1);
- tt_int_op(qes_match_hamming_max(NULL, NULL, 0, INT_MAX), ==, -1);
- tt_int_op(qes_match_hamming_max("ACTTG", "ACTTG", 0, -1), ==, -1);
- tt_int_op(qes_match_hamming_max("ACTTG", NULL, 0, -1), ==, -1);
- tt_int_op(qes_match_hamming_max(NULL, "ACTTG", 0, -1), ==, -1);
- tt_int_op(qes_match_hamming_max(NULL, NULL, 0, -1), ==, -1);
-end:
- ;
-}
-
-struct testcase_t qes_match_tests[] = {
- { "qes_match_hamming", test_qes_hamming, 0, NULL, NULL},
- { "qes_match_hamming_max", test_qes_hamming_max, 0, NULL, NULL},
- END_OF_TESTCASES
-};
diff --git a/src/libqes/test/test_seq.c b/src/libqes/test/test_seq.c
deleted file mode 100644
index c9dca23..0000000
--- a/src/libqes/test/test_seq.c
+++ /dev/null
@@ -1,500 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: test_seq.c
- *
- * Description: Test qes_seq.c
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "tests.h"
-#include <qes_seq.h>
-
-
-static void
-test_qes_seq_create (void *ptr)
-{
- struct qes_seq *seq = NULL;
- (void) ptr;
- tt_ptr_op(seq, ==, NULL);
- seq = qes_seq_create();
- tt_ptr_op(seq, !=, NULL);
- tt_ptr_op(seq->name.str, !=, NULL);
- tt_int_op(seq->name.capacity, >, 0);
- tt_int_op(seq->name.len, ==, 0);
- tt_ptr_op(seq->comment.str, !=, NULL);
- tt_int_op(seq->comment.capacity, >, 0);
- tt_int_op(seq->comment.len, ==, 0);
- tt_ptr_op(seq->seq.str, !=, NULL);
- tt_int_op(seq->seq.capacity, >, 0);
- tt_int_op(seq->seq.len, ==, 0);
- tt_ptr_op(seq->qual.str, !=, NULL);
- tt_int_op(seq->qual.capacity, >, 0);
- tt_int_op(seq->qual.len, ==, 0);
- tt_assert(qes_str_ok(&seq->name));
- tt_assert(qes_str_ok(&seq->comment));
- tt_assert(qes_str_ok(&seq->seq));
- tt_assert(qes_str_ok(&seq->qual));
-end:
- qes_seq_destroy(seq);
-}
-
-static void
-test_qes_seq_create_no_qual (void *ptr)
-{
- struct qes_seq *seq = NULL;
- (void) ptr;
- tt_ptr_op(seq, ==, NULL);
- seq = qes_seq_create_no_qual();
- tt_ptr_op(seq, !=, NULL);
- tt_ptr_op(seq->name.str, !=, NULL);
- tt_int_op(seq->name.capacity, >, 0);
- tt_int_op(seq->name.len, ==, 0);
- tt_ptr_op(seq->comment.str, !=, NULL);
- tt_int_op(seq->comment.capacity, >, 0);
- tt_int_op(seq->comment.len, ==, 0);
- tt_ptr_op(seq->seq.str, !=, NULL);
- tt_int_op(seq->seq.capacity, >, 0);
- tt_int_op(seq->seq.len, ==, 0);
- tt_ptr_op(seq->qual.str, ==, NULL);
- tt_int_op(seq->qual.capacity, ==, 0);
- tt_int_op(seq->qual.len, ==, 0);
- tt_assert(qes_str_ok(&seq->name));
- tt_assert(qes_str_ok(&seq->comment));
- tt_assert(qes_str_ok(&seq->seq));
- tt_assert(!qes_str_ok(&seq->qual));
-end:
- qes_seq_destroy(seq);
-}
-
-static void
-test_qes_seq_create_no_qual_or_comment (void *ptr)
-{
- struct qes_seq *seq = NULL;
- (void) ptr;
- tt_ptr_op(seq, ==, NULL);
- seq = qes_seq_create_no_qual_or_comment();
- tt_ptr_op(seq, !=, NULL);
- tt_ptr_op(seq->name.str, !=, NULL);
- tt_int_op(seq->name.capacity, >, 0);
- tt_int_op(seq->name.len, ==, 0);
- tt_ptr_op(seq->comment.str, ==, NULL);
- tt_int_op(seq->comment.capacity, ==, 0);
- tt_int_op(seq->comment.len, ==, 0);
- tt_ptr_op(seq->seq.str, !=, NULL);
- tt_int_op(seq->seq.capacity, >, 0);
- tt_int_op(seq->seq.len, ==, 0);
- tt_ptr_op(seq->qual.str, ==, NULL);
- tt_int_op(seq->qual.capacity, ==, 0);
- tt_int_op(seq->qual.len, ==, 0);
- tt_assert(qes_str_ok(&seq->name));
- tt_assert(!qes_str_ok(&seq->comment));
- tt_assert(qes_str_ok(&seq->seq));
- tt_assert(!qes_str_ok(&seq->qual));
-end:
- qes_seq_destroy(seq);
-}
-
-static void
-test_qes_seq_ok (void *ptr)
-{
- struct qes_seq *seq = NULL;
- (void) ptr;
- /* Test null seq */
- tt_assert(!qes_seq_ok(seq));
- /* Make valid seq */
- seq = qes_seq_create();
- tt_assert(qes_seq_ok(seq));
- /* invalidate name, should fail */
- qes_str_destroy_cp(&seq->name);
- tt_assert(!qes_seq_ok(seq));
- qes_seq_destroy(seq);
- /* remake */
- seq = qes_seq_create();
- tt_assert(qes_seq_ok(seq));
- /* invalidate comment, should fail */
- qes_str_destroy_cp(&seq->comment);
- tt_assert(!qes_seq_ok(seq));
- qes_seq_destroy(seq);
- /* remake */
- seq = qes_seq_create();
- tt_assert(qes_seq_ok(seq));
- /* invalidate seq, should fail */
- qes_str_destroy_cp(&seq->seq);
- tt_assert(!qes_seq_ok(seq));
- qes_seq_destroy(seq);
- /* remake */
- seq = qes_seq_create();
- tt_assert(qes_seq_ok(seq));
- /* invalidate qual, should fail */
- qes_str_destroy_cp(&seq->qual);
- tt_assert(!qes_seq_ok(seq));
- qes_seq_destroy(seq);
- /* Destroy seq, invalidating it */
- qes_seq_destroy(seq);
- tt_assert(!qes_seq_ok(seq));
-end:
- qes_seq_destroy(seq);
-}
-
-static void
-test_qes_seq_ok_no_comment (void *ptr)
-{
- struct qes_seq *seq = NULL;
-
- (void) ptr;
- /* Test null seq */
- tt_assert(!qes_seq_ok_no_comment(seq));
- /* Make valid seq */
- seq = qes_seq_create();
- tt_assert(qes_seq_ok_no_comment(seq));
- /* invalidate name, should fail */
- qes_str_destroy_cp(&seq->name);
- tt_assert(!qes_seq_ok_no_comment(seq));
- qes_seq_destroy(seq);
- /* remake */
- seq = qes_seq_create();
- tt_assert(qes_seq_ok_no_comment(seq));
- /* invalidate comment, should still pass */
- qes_str_destroy_cp(&seq->comment);
- tt_assert(qes_seq_ok_no_comment(seq));
- qes_seq_destroy(seq);
- /* remake */
- seq = qes_seq_create();
- tt_assert(qes_seq_ok_no_comment(seq));
- /* invalidate seq, should fail */
- qes_str_destroy_cp(&seq->seq);
- tt_assert(!qes_seq_ok_no_comment(seq));
- qes_seq_destroy(seq);
- /* remake */
- seq = qes_seq_create();
- tt_assert(qes_seq_ok_no_comment(seq));
- /* invalidate qual, should fail */
- qes_str_destroy_cp(&seq->qual);
- tt_assert(!qes_seq_ok_no_comment(seq));
- qes_seq_destroy(seq);
- /* Destroy seq, invalidating it */
- qes_seq_destroy(seq);
- tt_assert(!qes_seq_ok_no_comment(seq));
-end:
- qes_seq_destroy(seq);
-}
-
-static void
-test_qes_seq_ok_no_qual (void *ptr)
-{
- struct qes_seq *seq = NULL;
- (void) ptr;
- /* Test null seq */
- tt_assert(!qes_seq_ok_no_qual(seq));
- /* Make valid seq */
- seq = qes_seq_create();
- tt_assert(qes_seq_ok_no_qual(seq));
- /* invalidate name, should fail */
- qes_str_destroy_cp(&seq->name);
- tt_assert(!qes_seq_ok_no_qual(seq));
- qes_seq_destroy(seq);
- /* remake */
- seq = qes_seq_create();
- tt_assert(qes_seq_ok_no_qual(seq));
- /* invalidate comment, should fail */
- qes_str_destroy_cp(&seq->comment);
- tt_assert(!qes_seq_ok_no_qual(seq));
- qes_seq_destroy(seq);
- /* remake */
- seq = qes_seq_create();
- tt_assert(qes_seq_ok_no_qual(seq));
- /* invalidate seq, should fail */
- qes_str_destroy_cp(&seq->seq);
- tt_assert(!qes_seq_ok_no_qual(seq));
- qes_seq_destroy(seq);
- /* remake */
- seq = qes_seq_create();
- tt_assert(qes_seq_ok_no_qual(seq));
- /* invalidate qual, should PASS */
- qes_str_destroy_cp(&seq->qual);
- tt_assert(qes_seq_ok_no_qual(seq));
- qes_seq_destroy(seq);
- /* Destroy seq, invalidating it */
- qes_seq_destroy(seq);
- tt_assert(!qes_seq_ok_no_qual(seq));
-end:
- qes_seq_destroy(seq);
-}
-
-static void
-test_qes_seq_print(void *ptr)
-{
- struct qes_seq *seq = NULL;
- FILE *fp = NULL;
- char *outfile = NULL;
- char *truthfile = NULL;
- int res = 1;
-
- (void) ptr;
- /* Create output file */
- outfile = get_writable_file();
- fp = fopen(outfile, "w");
- tt_ptr_op(fp, !=, NULL);
- /* create sequence, fill it */
- seq = qes_seq_create();
- res = qes_seq_fill(seq, "TEST", "Comment 1", "AGCT", "IIII");
- tt_int_op(res, ==, 0);
- /* Print the seq to the output file */
- res = qes_seq_print(seq, fp, false, 0);
- tt_int_op(res, ==, 0);
- /* Check printing */
- truthfile = find_data_file("truth/qes_seq_print.fq");
- tt_ptr_op(truthfile, !=, NULL);
- tt_int_op(filecmp(outfile, truthfile), ==, 0);
- /* Clean up */
- free(truthfile);
- truthfile = NULL;
- fclose(fp);
- fp = NULL;
- qes_seq_destroy(seq);
-
- /* recreate, just without quality */
- seq = qes_seq_create();
- fp = fopen(outfile, "w");
- tt_ptr_op(fp, !=, NULL);
- res = qes_seq_fill(seq, "TEST", "Comment 1", "AGCT", "");
- tt_int_op(res, ==, 0);
- /* Print the seq to the output file */
- res = qes_seq_print(seq, fp, true, 0);
- tt_int_op(res, ==, 0);
- /* Check printing */
- truthfile = find_data_file("truth/qes_seq_print.fa");
- tt_ptr_op(truthfile, !=, NULL);
- tt_int_op(filecmp(outfile, truthfile), ==, 0);
- free(truthfile);
- truthfile = NULL;
- fclose(fp);
- fp = NULL;
-
- /* error cases */
- tt_int_op(qes_seq_print(NULL, stdout, false, 0), ==, 1);
- tt_int_op(qes_seq_print(seq, NULL, false, 0), ==, 1);
-
-end:
- qes_seq_destroy(seq);
- if (fp != NULL) fclose(fp);
- if (outfile != NULL) free(outfile);
- if (truthfile != NULL) free(truthfile);
-}
-
-static void
-test_qes_seq_ok_no_comment_or_qual (void *ptr)
-{
- struct qes_seq *seq = NULL;
-
- (void) ptr;
- /* Test null seq */
- tt_assert(!qes_seq_ok_no_comment_or_qual(seq));
- /* Make valid seq */
- seq = qes_seq_create();
- tt_assert(qes_seq_ok_no_comment_or_qual(seq));
- /* invalidate name, should fail */
- qes_str_destroy_cp(&seq->name);
- tt_assert(!qes_seq_ok_no_comment_or_qual(seq));
- qes_seq_destroy(seq);
- /* remake */
- seq = qes_seq_create();
- tt_assert(qes_seq_ok_no_comment_or_qual(seq));
- /* invalidate comment, should still pass */
- qes_str_destroy_cp(&seq->comment);
- tt_assert(qes_seq_ok_no_comment_or_qual(seq));
- qes_seq_destroy(seq);
- /* remake */
- seq = qes_seq_create();
- tt_assert(qes_seq_ok_no_comment_or_qual(seq));
- /* invalidate seq, should fail */
- qes_str_destroy_cp(&seq->seq);
- tt_assert(!qes_seq_ok_no_comment_or_qual(seq));
- qes_seq_destroy(seq);
- /* remake */
- seq = qes_seq_create();
- tt_assert(qes_seq_ok_no_comment_or_qual(seq));
- /* invalidate qual, should fail */
- qes_str_destroy_cp(&seq->qual);
- tt_assert(qes_seq_ok_no_comment_or_qual(seq));
- qes_seq_destroy(seq);
- /* Destroy seq, invalidating it */
- qes_seq_destroy(seq);
- tt_assert(!qes_seq_ok_no_comment_or_qual(seq));
-end:
- qes_seq_destroy(seq);
-}
-
-
-static void
-test_qes_seq_destroy (void *ptr)
-{
- struct qes_seq *seq = NULL;
-
- (void) ptr;
- tt_ptr_op(seq, ==, NULL);
- seq = qes_seq_create();
- tt_ptr_op(seq, !=, NULL);
- qes_seq_destroy(seq);
- tt_ptr_op(seq, ==, NULL);
- seq = NULL; /* Best be sure */
- qes_seq_destroy(seq);
-end:
- qes_seq_destroy(seq);
-}
-
-static void
-test_qes_seq_copy(void *ptr)
-{
- struct qes_seq *seq = NULL;
- struct qes_seq *copy = NULL;
- int res = 1;
-
- (void) ptr;
- seq = qes_seq_create();
- copy = qes_seq_create();
- res = qes_seq_fill(seq, "TEST", "Comment 1", "AGCT", "IIII");
- tt_int_op(res, ==, 0);
- tt_str_op(seq->name.str, ==, "TEST");
- tt_str_op(seq->comment.str, ==, "Comment 1");
- tt_str_op(seq->seq.str, ==, "AGCT");
- tt_str_op(seq->qual.str, ==, "IIII");
- res = qes_seq_copy(copy, seq);
- tt_int_op(res, ==, 0);
- tt_str_op(copy->name.str, ==, "TEST");
- tt_str_op(copy->comment.str, ==, "Comment 1");
- tt_str_op(copy->seq.str, ==, "AGCT");
- tt_str_op(copy->qual.str, ==, "IIII");
- tt_int_op(qes_seq_copy(NULL, seq), ==, 1);
- tt_int_op(qes_seq_copy(seq, NULL), ==, 1);
- tt_int_op(qes_seq_copy(seq, seq), ==, 1);
-
-end:
- qes_seq_destroy(seq);
- qes_seq_destroy(copy);
-}
-
-static void
-test_qes_seq_fill_funcs(void *ptr)
-{
-#define CHECK_FILLING(submember, st, ln) \
- seq = qes_seq_create(); \
- tt_str_op(seq->submember.str, ==, ""); \
- res = qes_seq_fill_ ##submember (seq, st, ln); \
- tt_int_op(res, ==, 0); \
- tt_str_op(seq->submember.str, ==, st); \
- tt_int_op(seq->submember.len, ==, ln); \
- tt_int_op(seq->submember.capacity, >=, ln); \
- qes_seq_destroy(seq);
-#define CHECK_FILLING_FAIL(submember, st, ln) \
- seq = qes_seq_create(); \
- tt_str_op(seq->submember.str, ==, ""); \
- res = qes_seq_fill_ ##submember (seq, st, ln); \
- tt_int_op(res, ==, 1); \
- tt_str_op(seq->submember.str, ==, ""); \
- tt_int_op(seq->submember.len, ==, 0); \
- qes_seq_destroy(seq);
-
- struct qes_seq *seq = NULL;
- int res = 0;
- char *tmp = NULL;
-
- (void) ptr;
- /* These should all work pretty well */
- CHECK_FILLING(name, "HWI_TEST", 8)
- CHECK_FILLING(comment, "abc 123 comment", 15)
- CHECK_FILLING(seq, "ACTG", 4)
- CHECK_FILLING(qual, "IIII", 4)
- /* These should all fail */
- CHECK_FILLING_FAIL(name, NULL, 1)
- CHECK_FILLING_FAIL(name, "BAD", 0)
- CHECK_FILLING_FAIL(comment, NULL, 1)
- CHECK_FILLING_FAIL(comment, "BAD", 0)
- CHECK_FILLING_FAIL(seq, NULL, 1)
- CHECK_FILLING_FAIL(seq, "BAD", 0)
- CHECK_FILLING_FAIL(qual, NULL, 1)
- CHECK_FILLING_FAIL(qual, "BAD", 0)
- tt_int_op(qes_seq_fill_name(NULL, "BAD", 3), ==, 1);
- tt_int_op(qes_seq_fill_comment(NULL, "BAD", 3), ==, 1);
- tt_int_op(qes_seq_fill_seq(NULL, "BAD", 3), ==, 1);
- tt_int_op(qes_seq_fill_qual(NULL, "BAD", 3), ==, 1);
-
- /* Fill header */
-#define CHECK_FILL_HEADER(st, ln, nm, nmlen, com, comlen) \
- tmp = strdup(st); \
- seq = qes_seq_create(); \
- tt_str_op(seq->name.str, ==, ""); \
- tt_str_op(seq->comment.str, ==, ""); \
- res = qes_seq_fill_header(seq, tmp, ln); \
- tt_int_op(res, ==, 0); \
- tt_str_op(seq->name.str, ==, nm); \
- tt_int_op(seq->name.len, ==, nmlen); \
- tt_int_op(seq->name.capacity, >=, nmlen); \
- tt_str_op(seq->comment.str, ==, com); \
- tt_int_op(seq->comment.len, ==, comlen); \
- tt_int_op(seq->comment.capacity, >=, comlen); \
- qes_seq_destroy(seq); \
- free(tmp); \
- tmp = NULL;
- CHECK_FILL_HEADER("@HWI_TEST COMM\n", 15, "HWI_TEST", 8, "COMM", 4)
- CHECK_FILL_HEADER("@HWI_TEST COMM\n", 0, "HWI_TEST", 8, "COMM", 4)
- CHECK_FILL_HEADER("@HWI_TEST COMM \r\n", 17, "HWI_TEST", 8, "COMM", 4)
- CHECK_FILL_HEADER("@HWI_TEST COMM", 14, "HWI_TEST", 8, "COMM", 4)
- CHECK_FILL_HEADER(">HWI_TEST COMM", 14, "HWI_TEST", 8, "COMM", 4)
- CHECK_FILL_HEADER("HWI_TEST COMM", 13, "HWI_TEST", 8, "COMM", 4)
- CHECK_FILL_HEADER("@HWI_TEST", 9, "HWI_TEST", 8, "", 0)
- CHECK_FILL_HEADER(">HWI_TEST", 9, "HWI_TEST", 8, "", 0)
- CHECK_FILL_HEADER("HWI_TEST", 8, "HWI_TEST", 8, "", 0)
- /* Check bad values */
- seq = qes_seq_create();
- tmp = strdup("BAD");
- tt_int_op(qes_seq_fill_header(NULL, tmp, 3), ==, 1);
- tt_int_op(qes_seq_fill_header(seq, NULL, 3), ==, 1);
- qes_seq_destroy(seq);
-end:
- if (tmp != NULL) {
- free(tmp);
- }
- qes_seq_destroy(seq);
-#undef CHECK_FILLING
-#undef CHECK_FILLING_FAIL
-#undef CHECK_FILL_HEADER
-}
-
-
-struct testcase_t qes_seq_tests[] = {
- { "qes_seq_create", test_qes_seq_create, 0, NULL, NULL},
- { "qes_seq_create_no_qual", test_qes_seq_create_no_qual, 0, NULL, NULL},
- { "qes_seq_create_no_qual_or_comment",
- test_qes_seq_create_no_qual_or_comment, 0, NULL, NULL},
- { "qes_seq_ok", test_qes_seq_ok, 0, NULL, NULL},
- { "qes_seq_ok_no_comment", test_qes_seq_ok_no_comment, 0, NULL, NULL},
- { "qes_seq_ok_no_qual", test_qes_seq_ok_no_qual, 0, NULL, NULL},
- { "qes_seq_ok_no_comment_or_qual", test_qes_seq_ok_no_comment_or_qual, 0,
- NULL, NULL},
- { "qes_seq_destroy", test_qes_seq_destroy, 0, NULL, NULL},
- { "qes_seq_fill", test_qes_seq_fill_funcs, 0, NULL, NULL},
- { "qes_seq_copy", test_qes_seq_copy, 0, NULL, NULL},
- { "qes_seq_print", test_qes_seq_print, 0, NULL, NULL},
- END_OF_TESTCASES
-};
diff --git a/src/libqes/test/test_seqcats.sh b/src/libqes/test/test_seqcats.sh
deleted file mode 100644
index 120bc92..0000000
--- a/src/libqes/test/test_seqcats.sh
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/bin/bash
-
-if [ $# -lt 1 ]
-then
- files=("data/test.fasta")
-else
- files=( "$@" )
-fi
-
-for file in "${files[@]}"
-do
- kseq_m5=$(bin/kseqcat $file | md5sum | awk '{print $1}')
- qseq_m5=$(bin/qes_seqcat $file | md5sum | awk '{print $1}')
- kprint_m5=$(bin/kseqcat $file | seqtk seq -l 79 | md5sum | awk '{print $1}')
- qprint_m5=$(bin/qes_seqprint $file | md5sum | awk '{print $1}')
-
- if [ "$kseq_m5" != "$qseq_m5" ]
- then
- echo "TEST (seq) FAILED: $file"
- echo " kseq: $kseq_m5"
- echo " qes: $qseq_m5"
- else
- echo "TEST (seq) PASSED: $file"
- fi
-
- if [ "$kprint_m5" != "$qprint_m5" ]
- then
- echo "TEST (print) FAILED: $file"
- echo " kseq: $kprint_m5"
- echo " qes: $qprint_m5"
- else
- echo "TEST (print) PASSED: $file"
- fi
-done
diff --git a/src/libqes/test/test_seqfile.c b/src/libqes/test/test_seqfile.c
deleted file mode 100644
index 710ea60..0000000
--- a/src/libqes/test/test_seqfile.c
+++ /dev/null
@@ -1,418 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: test_seqfile.c
- *
- * Description: Tests for the qes_seqfile module
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "tests.h"
-#include <qes_seqfile.h>
-#include "kseq.h"
-
-
-#ifdef ZLIB_FOUND
-# include <zlib.h>
- KSEQ_INIT(gzFile, gzread)
-#else
-# include <sys/stat.h>
-# include <fcntl.h>
- KSEQ_INIT(int, read)
-#endif
-
-
-
-static void
-test_qes_seqfile_create(void *ptr)
-{
- struct qes_seqfile *sf = NULL;
- char *fname = NULL;
-
- (void) ptr;
- /* Test file opening for reading */
- /* test opening a valid, unziped FASTQ */
- fname = find_data_file("test.fastq");
- tt_assert(fname != NULL);
- sf = qes_seqfile_create(fname, "r");
- tt_ptr_op(sf, !=, NULL);
- tt_ptr_op(sf->qf, !=, NULL);
- tt_int_op(sf->qf->mode, ==, QES_FILE_MODE_READ);
- tt_int_op(sf->n_records, ==, 0);
- tt_int_op(sf->format, ==, FASTQ_FMT);
- qes_seqfile_destroy(sf);
- free(fname);
- /* test opening a valid, unziped FASTA */
- fname = find_data_file("test.fasta");
- tt_assert(fname != NULL);
- sf = qes_seqfile_create(fname, "r");
- tt_ptr_op(sf, !=, NULL);
- tt_ptr_op(sf->qf, !=, NULL);
- tt_int_op(sf->qf->mode, ==, QES_FILE_MODE_READ);
- tt_int_op(sf->n_records, ==, 0);
- tt_int_op(sf->format, ==, FASTA_FMT);
- qes_seqfile_destroy(sf);
- free(fname);
- /* Test opening a file in transparent write mode */
- fname = get_writable_file();
- tt_assert(fname != NULL);
- sf = qes_seqfile_create(fname, "wT");
- QES_ZWRITE(sf->qf->fp, "ABCD", 4);
- tt_ptr_op(sf, !=, NULL);
- tt_ptr_op(sf->qf, !=, NULL);
- tt_int_op(sf->qf->mode, ==, QES_FILE_MODE_WRITE);
- tt_int_op(sf->n_records, ==, 0);
- tt_int_op(access(fname, F_OK), ==, 0);
- qes_seqfile_destroy(sf);
- clean_writable_file(fname);
- fname = NULL;
- /* Test opening a file in write mode , acually zipping output */
- fname = get_writable_file();
- tt_assert(fname != NULL);
- sf = qes_seqfile_create(fname, "w9");
- tt_ptr_op(sf, !=, NULL);
- tt_ptr_op(sf->qf, !=, NULL);
- tt_int_op(sf->qf->mode, ==, QES_FILE_MODE_WRITE);
- tt_int_op(sf->n_records, ==, 0);
- tt_int_op(access(fname, F_OK), ==, 0);
- qes_seqfile_destroy(sf);
- clean_writable_file(fname);
- fname = NULL;
-end:
- qes_seqfile_destroy(sf);
- if (fname != NULL) {
- free(fname);
- }
-}
-
-
-static void
-test_qes_seqfile_guess_format (void *ptr)
-{
- struct qes_seqfile *sf = NULL;
- int res = -1;
- char *fname = NULL;
-
- (void) ptr;
- /* Test file opening for reading */
- fname = find_data_file("test.fastq");
- tt_assert(fname != NULL);
- sf = qes_seqfile_create(fname, "r");
- /* test with a FASTQ file */
- res = qes_seqfile_guess_format(sf);
- tt_int_op(res, ==, FASTQ_FMT);
- tt_int_op(sf->format, ==, FASTQ_FMT);
- qes_seqfile_destroy(sf);
- free(fname);
- /* test with a FASTA file */
- fname = find_data_file("test.fasta");
- tt_assert(fname != NULL);
- sf = qes_seqfile_create(fname, "r");
- res = qes_seqfile_guess_format(sf);
- tt_int_op(res, ==, FASTA_FMT);
- tt_int_op(sf->format, ==, FASTA_FMT);
- qes_seqfile_destroy(sf);
- free(fname);
- fname = NULL;
-#ifdef ZLIB_FOUND
- /* test with a gziped FASTQ file */
- fname = find_data_file("test.fastq.gz");
- tt_assert(fname != NULL);
- sf = qes_seqfile_create(fname, "r");
- res = qes_seqfile_guess_format(sf);
- tt_int_op(res, ==, FASTQ_FMT);
- tt_int_op(sf->format, ==, FASTQ_FMT);
- qes_seqfile_destroy(sf);
-#endif
-end:
- qes_seqfile_destroy(sf);
- if (fname != NULL) free(fname);
-}
-
-
-static void
-test_qes_seqfile_destroy (void *ptr)
-{
- struct qes_seqfile *sf = NULL;
- char *fname = NULL;
-
- (void) ptr;
- /* Test file opening for reading */
- fname = find_data_file("test.fastq");
- tt_assert(fname != NULL);
- sf = qes_seqfile_create(fname, "r");
- tt_ptr_op(sf, !=, NULL);
- tt_assert(qes_seqfile_ok(sf));
- qes_seqfile_destroy(sf);
- tt_ptr_op(sf, ==, NULL);
- tt_assert(!qes_seqfile_ok(sf));
-end:
- qes_seqfile_destroy(sf);
- if (fname != NULL) free(fname);
-}
-
-
-/*=== FUNCTION ============================================================*
-Name: test_qes_seqfile_read
-Description: Tests the qes_seqfile_read function from qes_seqfile.c
- *===========================================================================*/
-static void
-test_qes_seqfile_read (void *ptr)
-{
- struct qes_seq *seq = qes_seq_create();
- ssize_t res = 0;
- struct qes_seqfile *sf = NULL;
- char *fname = NULL;
- /* Check a seq is empty */
-#define CHECK_SEQ_EMPTY \
- tt_str_op(seq->name.str, ==, ""); \
- tt_str_op(seq->comment.str, ==, ""); \
- tt_str_op(seq->seq.str, ==, ""); \
- tt_str_op(seq->qual.str, ==, "")
- /* Check seq against the first known read */
-#define CHECK_SEQ_FIRST \
- tt_str_op(seq->name.str, ==, first_fastq_read[0]); \
- tt_str_op(seq->comment.str, ==, first_fastq_read[1]); \
- tt_str_op(seq->seq.str, ==, first_fastq_read[2]); \
- tt_str_op(seq->qual.str, ==, first_fastq_read[3])
- /* Open, read, check & close a seqfile */
-#define CHECK_SEQFILE_READ(fn, expt_res, check_seq) \
- fname = find_data_file(fn); \
- tt_assert(fname != NULL); \
- sf = qes_seqfile_create(fname, "r"); \
- res = qes_seqfile_read(sf, seq); \
- tt_int_op(res, ==, expt_res); \
- check_seq; \
- qes_seqfile_destroy(sf); \
- free(fname); \
- fname = NULL
- /* Open, read, check & close a seqfile, forcing its filetype to FASTQ */
-#define CHECK_SEQFILE_READ_FORCE(fn, expt_res, check_seq) \
- fname = find_data_file(fn); \
- tt_assert(fname != NULL); \
- sf = qes_seqfile_create(fname, "r"); \
- qes_seqfile_set_format(sf, FASTQ_FMT); \
- res = qes_seqfile_read(sf, seq); \
- tt_int_op(res, ==, expt_res); \
- check_seq; \
- qes_seqfile_destroy(sf); \
- free(fname); \
- fname = NULL
-
- (void) ptr;
- /* Test file opening for reading */
- CHECK_SEQFILE_READ("test.fastq", first_fastq_len, CHECK_SEQ_FIRST);
- CHECK_SEQFILE_READ("test.fasta", 33,
- tt_str_op(seq->name.str, ==, "HWI-ST960:105:D10GVACXX:2:1101:1122:2186");
- tt_str_op(seq->comment.str, ==, "1:N:0: bcd:RPI8 seq:CACACTTGAATC");
- tt_str_op(seq->seq.str, ==, "CACACTTGAATCCAGTTTAAAGTTAACTCATTG");
- tt_int_op(seq->qual.len, ==, 0);
- tt_str_op(seq->qual.str, ==, "")
- );
- CHECK_SEQFILE_READ("nocomment.fasta", 33,
- tt_str_op(seq->name.str, ==, "HWI-ST960:105:D10GVACXX:2:1101:1122:2186");
- tt_int_op(seq->comment.len, ==, 0);
- tt_str_op(seq->comment.str, ==, "");
- tt_str_op(seq->seq.str, ==, "CACACTTGAATCCAGTTTAAAGTTAACTCATTG");
- tt_int_op(seq->qual.len, ==, 0);
- tt_str_op(seq->qual.str, ==, "")
- );
- /* Test with bad fastqs, ensure all code paths are taken */
- CHECK_SEQFILE_READ("loremipsum.txt", -2, CHECK_SEQ_EMPTY);
- CHECK_SEQFILE_READ("bad_nohdr.fastq", -2, CHECK_SEQ_EMPTY);
- CHECK_SEQFILE_READ("loremipsum.txt", -2, CHECK_SEQ_EMPTY);
- CHECK_SEQFILE_READ_FORCE("loremipsum.txt", -3, CHECK_SEQ_EMPTY);
- CHECK_SEQFILE_READ("empty.fastq", -3, CHECK_SEQ_EMPTY);
- CHECK_SEQFILE_READ("bad_noqual.fastq", -6, CHECK_SEQ_EMPTY);
- CHECK_SEQFILE_READ("bad_noqualhdrchr.fastq", -5, CHECK_SEQ_EMPTY);
- CHECK_SEQFILE_READ("bad_noqualhdreol.fastq", -5, CHECK_SEQ_EMPTY);
- CHECK_SEQFILE_READ("bad_diff_lens.fastq", -7, CHECK_SEQ_EMPTY);
- /* Check with bad params that it returns -2 */
- res = qes_seqfile_read(NULL, seq);
- tt_int_op(res, ==, -2);
- res = qes_seqfile_read(sf, NULL);
- tt_int_op(res, ==, -2);
-end:
- qes_seqfile_destroy(sf);
- qes_seq_destroy(seq);
- if (fname != NULL) {
- free(fname);
- }
-#undef CHECK_SEQ_EMPTY
-#undef CHECK_SEQFILE_READ
-}
-
-
-static void
-test_qes_seqfile_read_vs_kseq (void *ptr)
-{
- struct qes_seq *seq = qes_seq_create();
-#ifdef ZLIB_FOUND
- char *fname = find_data_file("test.fastq.gz");
- gzFile fp = gzopen(fname, "r");
-#else
- char *fname = find_data_file("test.fastq");
- int fp = open(fname, O_RDONLY);
-#endif
- struct qes_seqfile *sf = qes_seqfile_create(fname, "r");
- kseq_t *kseq = kseq_init(fp);
- ssize_t kseq_res = 0;
- ssize_t my_res = 0;
-
- (void) ptr;
- tt_assert(fname != NULL);
- while (1) {
- my_res = qes_seqfile_read(sf, seq);
- kseq_res = kseq_read(kseq);
- tt_int_op(my_res, ==, kseq_res);
- if (my_res < 1 || kseq_res < 1) {
- /* EOF or error */
- break;
- }
- tt_str_op(seq->name.str, ==, kseq->name.s);
- tt_str_op(seq->comment.str, ==, kseq->comment.s);
- tt_str_op(seq->seq.str, ==, kseq->seq.s);
- tt_str_op(seq->qual.str, ==, kseq->qual.s);
- }
- my_res = qes_seqfile_read(sf, seq);
- kseq_res = kseq_read(kseq);
- tt_int_op(my_res, ==, kseq_res);
- tt_int_op(my_res, ==, EOF);
- qes_seqfile_destroy(sf);
- qes_seq_destroy(seq);
- kseq_destroy(kseq);
- kseq = NULL;
-#ifdef ZLIB_FOUND
- gzclose(fp);
-#else
- close(fp);
-#endif
- free(fname);
- /* Try again, with fasta */
- seq = qes_seq_create();
- fname = find_data_file("test_large.fasta.gz");
- tt_assert(fname != NULL);
- sf = qes_seqfile_create(fname, "r");
-#ifdef ZLIB_FOUND
- fp = gzopen(fname, "r");
-#else
- fp = open(fname, O_RDONLY);
-#endif
- kseq = kseq_init(fp);
- while (1) {
- my_res = qes_seqfile_read(sf, seq);
- kseq_res = kseq_read(kseq);
- tt_int_op(my_res, ==, kseq_res);
- if (my_res < 1 || kseq_res < 1) {
- /* EOF or error */
- break;
- }
- tt_str_op(seq->name.str, ==, kseq->name.s);
- tt_str_op(seq->comment.str, ==, kseq->comment.s);
- tt_str_op(seq->seq.str, ==, kseq->seq.s);
- }
-end:
- qes_seqfile_destroy(sf);
- qes_seq_destroy(seq);
- if (kseq != NULL) kseq_destroy(kseq);
- if (fname != NULL) free(fname);
-#ifdef ZLIB_FOUND
- gzclose(fp);
-#else
- close(fp);
-#endif
-}
-
-
-/*=== FUNCTION ============================================================*
-Name: test_qes_seqfile_write
-Description: Tests the qes_seqfile_write function from qes_seqfile.c
- *===========================================================================*/
-static void
-test_qes_seqfile_write (void *ptr)
-{
- struct qes_seq *seq = qes_seq_create();
- size_t expt_bytes = 0;
- ssize_t res = 0;
- struct qes_seqfile *sf = NULL;
- char *fname = NULL;
- char *crc = NULL;
-
- (void) ptr;
- /* Make a seq to write */
- qes_seq_fill_name(seq, "HWI-TEST", 8);
- qes_seq_fill_comment(seq, "testseq 1 2 3", 13);
- qes_seq_fill_seq(seq, "ACTCAATT", 8);
- qes_seq_fill_qual(seq, "IIIIIIII", 8);
- expt_bytes = 1 + 8 + 1 + 13 + 1 + /* @ + name + ' ' + comment + '\n' */
- 8 + 1 + 2 + 8 + 1; /* seq + '\n' + "+\n" + qual + '\n' */
- /* Test with a FASTQ seqfile */
- fname = get_writable_file();
- tt_assert(fname != NULL);
- sf = qes_seqfile_create(fname, "wT");
- qes_seqfile_set_format(sf, FASTQ_FMT);
- res = qes_seqfile_write(sf, seq);
- tt_int_op(res, ==, expt_bytes);
- qes_seqfile_destroy(sf); /* Has to happen here to flush it */
- crc = crc32_file(fname);
- tt_str_op(crc, ==, "d4665941");
- clean_writable_file(fname);
- free(crc);
- fname = NULL;
- crc = NULL;
- /* Test with a FASTA seqfile */
- expt_bytes = 1 + 8 + 1 + 13 + 1 + /* @ + name + ' ' + comment + '\n' */
- 8 + 1; /* seq + '\n'*/
- fname = get_writable_file();
- tt_assert(fname != NULL);
- sf = qes_seqfile_create(fname, "wT");
- qes_seqfile_set_format(sf, FASTA_FMT);
- /* do the write */
- res = qes_seqfile_write(sf, seq);
- tt_int_op(res, ==, expt_bytes);
- qes_seqfile_destroy(sf); /* Flush it */
- crc = crc32_file(fname);
- tt_str_op(crc, ==, "0a295c77");
- clean_writable_file(fname);
- fname = NULL;
- /* Check with bad params that it returns -2 */
- res = qes_seqfile_write(NULL, seq);
- tt_int_op(res, ==, -2);
- res = qes_seqfile_write(sf, NULL);
- tt_int_op(res, ==, -2);
-end:
- qes_seqfile_destroy(sf);
- qes_seq_destroy(seq);
- if (fname != NULL) free(fname);
- if (crc != NULL) free(crc);
-}
-
-
-struct testcase_t qes_seqfile_tests[] = {
- { "qes_seqfile_create", test_qes_seqfile_create, 0, NULL, NULL},
- { "qes_seqfile_guess_format", test_qes_seqfile_guess_format, 0, NULL, NULL},
- { "qes_seqfile_destroy", test_qes_seqfile_destroy, 0, NULL, NULL},
- { "qes_seqfile_read_vs_kseq", test_qes_seqfile_read_vs_kseq, 0, NULL, NULL},
- { "qes_seqfile_read", test_qes_seqfile_read, 0, NULL, NULL},
- { "qes_seqfile_write", test_qes_seqfile_write, 0, NULL, NULL},
- END_OF_TESTCASES
-};
diff --git a/src/libqes/test/test_sequtil.c b/src/libqes/test/test_sequtil.c
deleted file mode 100644
index 5eabd1c..0000000
--- a/src/libqes/test/test_sequtil.c
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: test_sequtil.c
- *
- * Description: Tests for the sequtil module
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "tests.h"
-#include <qes_sequtil.h>
-
-
-static void
-test_qes_sequtil_translate_codon (void *ptr)
-{
- size_t iii;
- size_t jjj;
- char *cdn = NULL;
- char aa = 0;
-
- (void) ptr;
- for (iii = 0; iii < n_codons; iii++) {
- aa = qes_sequtil_translate_codon(codon_list[iii]);
- tt_assert_op_type(aa, ==, aa_list[iii], char, "%c");
- }
- tt_int_op(qes_sequtil_translate_codon("XACACA"), ==, -1);
- tt_int_op(qes_sequtil_translate_codon("A"), ==, -1);
- tt_int_op(qes_sequtil_translate_codon(NULL), ==, -1);
- /* Try with mutations */
- for (iii = 0; iii < n_codons; iii++) {
- for (jjj = 0; jjj < 3; jjj++) {
- cdn = strdup(codon_list[iii]);
- cdn[jjj] = 'N';
- aa = qes_sequtil_translate_codon(cdn);
- tt_assert_op_type(aa, ==, 'X', char, "%c");
- free(cdn);
- cdn = NULL;
- }
- }
-end:
- if (cdn != NULL) free(cdn);
-}
-
-struct testcase_t qes_sequtil_tests[] = {
- { "qes_sequtil_translate_codon", test_qes_sequtil_translate_codon, 0, NULL, NULL},
- END_OF_TESTCASES
-};
diff --git a/src/libqes/test/test_util.c b/src/libqes/test/test_util.c
deleted file mode 100644
index da8a8c2..0000000
--- a/src/libqes/test/test_util.c
+++ /dev/null
@@ -1,161 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: test_util.c
- *
- * Description: Test qes_util.c
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "tests.h"
-#include <qes_util.h>
-
-
-/* Actual tests */
-static void
-test_qes_calloc(void *ptr)
-{
- void *res = NULL;
- const size_t bufsize = 1<<10;
- unsigned char *zeros[1<<10];
-
- (void) ptr;
- memset(zeros, 0, bufsize);
- /* This should work, and the buffer should be zero throughout */
- res = qes_calloc(1, 1);
- tt_ptr_op(res, !=, NULL);
- tt_int_op(memcmp(res, zeros, 1), ==, 0);
- free(res);
- res = NULL;
-end:
- if (res != NULL) free(res);
-}
-
-static void
-test_qes_malloc(void *ptr)
-{
- void *res = NULL;
-
- (void) ptr;
- res = qes_malloc(1);
- tt_ptr_op(res, !=, NULL);
- free(res);
- res = NULL;
-end:
- if (res != NULL) free(res);
-}
-
-static void
-test_qes_realloc(void *ptr)
-{
- char *res = NULL;
- const char *str = "test";
- char *dat = strdup(str);
-
- (void) ptr;
- /* Test resizing buffer */
- res = qes_realloc(dat, 10);
- dat = NULL;
- tt_ptr_op(res, !=, NULL);
- tt_int_op(memcmp(res, str, 5), ==, 0);
- free(res);
- res = NULL;
-end:
- if (res != NULL) free(res);
- if (dat != NULL) free(dat);
-}
-
-static void
-test_qes_free(void *ptr)
-{
- char *dat = strdup("test");
-
- (void) ptr;
- /* Test freeing buffer */
- tt_ptr_op(dat, !=, NULL);
- qes_free(dat);
- tt_ptr_op(dat, ==, NULL);
- /* This free(NULL) should not fail */
- qes_free(dat);
- tt_ptr_op(dat, ==, NULL);
-end:
- if (dat != NULL) free(dat);
-}
-
-static void
-test_qes_roundup32 (void *ptr)
-{
- int32_t val = 3;
- uint32_t uval = (1u<<31) - 1;
-
- (void) ptr;
- /* Signed */
- tt_int_op(qes_roundup32(val), ==, 4);
- val++;
- tt_int_op(qes_roundup32(val), ==, 8);
- val = 8;
- tt_int_op(qes_roundup32(val), ==, 16);
- val = 262143;
- tt_int_op(qes_roundup32(val), ==, 262144);
- /* Unsigned */
- tt_int_op(qes_roundup32(uval), ==, 1u<<31);
- uval++;
- tt_int_op(qes_roundup32(uval), ==, 0);
-end:
- ;
-}
-
-static void
-test_qes_roundup64 (void *ptr)
-{
- int64_t val = 3;
- uint64_t uval = (1llu<<63) - 1;
-
- (void) ptr;
- /* Signed */
- tt_int_op(qes_roundup64(val), ==, 4);
- val = 4;
- tt_int_op(qes_roundup64(val), ==, 8);
- val = 8;
- tt_int_op(qes_roundup64(val), ==, 16);
- val = 262143llu;
- tt_int_op(qes_roundup64(val), ==, 262144);
- /* Unsigned */
- tt_assert(qes_roundup64(uval) == 1llu<<63);
- uval = 1llu<<62;
- tt_assert(qes_roundup64(uval) == 1llu<<63);
- uval = 63llu;
- tt_assert(qes_roundup64(uval) - 2 == 62llu);
-end:
- ;
-}
-
-
-struct testcase_t qes_util_tests[] = {
- { "qes_calloc", test_qes_calloc, 0, NULL, NULL},
- { "qes_malloc", test_qes_malloc, 0, NULL, NULL},
- { "qes_realloc", test_qes_realloc, 0, NULL, NULL},
- { "qes_free", test_qes_free, 0, NULL, NULL},
- { "qes_roundup32", test_qes_roundup32, 0, NULL, NULL},
- { "qes_roundup64", test_qes_roundup64, 0, NULL, NULL},
- END_OF_TESTCASES
-};
diff --git a/src/libqes/test/testdata.c b/src/libqes/test/testdata.c
deleted file mode 100644
index 298abdf..0000000
--- a/src/libqes/test/testdata.c
+++ /dev/null
@@ -1,160 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: testdata.c
- *
- * Description: Data for tests
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "testdata.h"
-
-
-const size_t n_loremipsum_lines = 11;
-const size_t loremipsum_fsize = 80+76+80+75+80+79+77+75+69+1+20;
-const size_t loremipsum_line_lens[] = {
- 80, 76, 80, 75, 80, 79, 77, 75, 69, 1, 20
-};
-const char *loremipsum_lines[] = {
- "Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec ornare tortor et\n",
- "rhoncus iaculis. Sed suscipit, arcu nec elementum vestibulum, tortor tortor\n",
- "dictum dui, eu sodales magna orci eu libero. Cras commodo, ligula tempor auctor\n",
- "vulputate, eros urna gravida eros, eget congue leo quam quis mi. Curabitur\n",
- "luctus augue nibh, eget vehicula augue commodo eget. Donec condimentum molestie\n",
- "adipiscing. In non purus lacus. Nam nec mollis mauris. Donec rhoncus, diam sit\n",
- "amet rhoncus viverra, lectus risus tincidunt ipsum, in dignissim justo purus\n",
- "eget enim. Fusce congue nulla egestas est auctor faucibus. Integer feugiat\n",
- "molestie leo, a interdum neque pretium nec. Etiam sit amet nibh leo.\n",
- "\n",
- "End of lorem ipsum.\n",
-};
-const char *first_fastq_read[] = {
- "HWI-ST960:105:D10GVACXX:2:1101:1151:2158",
- "1:N:0: bcd:RPI9 seq:CACGATCAGATC",
- "CACGATCAGATCAANGACATTGAATCTATATGT",
- "JJJJJJJIJHIJCC#4ADFFHHHGHJJJJIJJJ",
-};
-const size_t first_fastq_len = 33;
-
-
-const size_t n_codons = 125;
-
-const char *codon_list[] = {
- "AAA", "AAC", "AAG", "AAT", "AAU",
- "ACA", "ACC", "ACG", "ACT", "ACU",
- "AGA", "AGC", "AGG", "AGT", "AGU",
- "ATA", "ATC", "ATG", "ATT", "ATU",
- "AUA", "AUC", "AUG", "AUT", "AUU",
- "CAA", "CAC", "CAG", "CAT", "CAU",
- "CCA", "CCC", "CCG", "CCT", "CCU",
- "CGA", "CGC", "CGG", "CGT", "CGU",
- "CTA", "CTC", "CTG", "CTT", "CTU",
- "CUA", "CUC", "CUG", "CUT", "CUU",
- "GAA", "GAC", "GAG", "GAT", "GAU",
- "GCA", "GCC", "GCG", "GCT", "GCU",
- "GGA", "GGC", "GGG", "GGT", "GGU",
- "GTA", "GTC", "GTG", "GTT", "GTU",
- "GUA", "GUC", "GUG", "GUT", "GUU",
- "TAA", "TAC", "TAG", "TAT", "TAU",
- "TCA", "TCC", "TCG", "TCT", "TCU",
- "TGA", "TGC", "TGG", "TGT", "TGU",
- "TTA", "TTC", "TTG", "TTT", "TTU",
- "TUA", "TUC", "TUG", "TUT", "TUU",
- "UAA", "UAC", "UAG", "UAT", "UAU",
- "UCA", "UCC", "UCG", "UCT", "UCU",
- "UGA", "UGC", "UGG", "UGT", "UGU",
- "UTA", "UTC", "UTG", "UTT", "UTU",
- "UUA", "UUC", "UUG", "UUT", "UUU",
-};
-
-const char aa_list[] = {
- 'K', 'N', 'K', 'N', 'N',
- 'T', 'T', 'T', 'T', 'T',
- 'R', 'S', 'R', 'S', 'S',
- 'I', 'I', 'M', 'I', 'I',
- 'I', 'I', 'M', 'I', 'I',
- 'Q', 'H', 'Q', 'H', 'H',
- 'P', 'P', 'P', 'P', 'P',
- 'R', 'R', 'R', 'R', 'R',
- 'L', 'L', 'L', 'L', 'L',
- 'L', 'L', 'L', 'L', 'L',
- 'E', 'D', 'E', 'D', 'D',
- 'A', 'A', 'A', 'A', 'A',
- 'G', 'G', 'G', 'G', 'G',
- 'V', 'V', 'V', 'V', 'V',
- 'V', 'V', 'V', 'V', 'V',
- '*', 'Y', '*', 'Y', 'Y',
- 'S', 'S', 'S', 'S', 'S',
- '*', 'C', 'W', 'C', 'C',
- 'L', 'F', 'L', 'F', 'F',
- 'L', 'F', 'L', 'F', 'F',
- '*', 'Y', '*', 'Y', 'Y',
- 'S', 'S', 'S', 'S', 'S',
- '*', 'C', 'W', 'C', 'C',
- 'L', 'F', 'L', 'F', 'F',
- 'L', 'F', 'L', 'F', 'F',
-};
-
-void
-test_data_files (void *ptr)
-{
- char *fname = NULL;
- char *crc_res = NULL;
-
- (void) ptr;
- fname = find_data_file("loremipsum.txt");
- crc_res = crc32_file(fname);
- tt_str_op(crc_res, ==, "9f20f7ec");
- free(fname);
- free(crc_res);
- fname = find_data_file("loremipsum.txt.gz");
- crc_res = crc32_file(fname);
- tt_str_op(crc_res, ==, "4e42dcb2");
- free(fname);
- free(crc_res);
- fname = find_data_file("test.fastq");
- crc_res = crc32_file(fname);
- tt_str_op(crc_res, ==, "c32cc3c0");
- free(fname);
- free(crc_res);
- fname = find_data_file("test.fasta");
- crc_res = crc32_file(fname);
- tt_str_op(crc_res, ==, "3de06bb6");
- free(fname);
- free(crc_res);
- fname = find_data_file("test.fastq.gz");
- crc_res = crc32_file(fname);
- tt_str_op(crc_res, ==, "ba1206ee");
- free(fname);
- free(crc_res);
- fname = find_data_file("test.fastq.bz2");
- crc_res = crc32_file(fname);
- tt_str_op(crc_res, ==, "c8b66d33");
-end:
- free(fname);
- free(crc_res);
-}
-
-struct testcase_t data_tests[] = {
- { "data_files", test_data_files, 0, NULL, NULL},
- END_OF_TESTCASES
-};
diff --git a/src/libqes/test/testdata.h b/src/libqes/test/testdata.h
deleted file mode 100644
index 68ab280..0000000
--- a/src/libqes/test/testdata.h
+++ /dev/null
@@ -1,65 +0,0 @@
-/*
- * Copyright 2015 Kevin Murray <spam at kdmurray.id.au>
- *
- * This program is free software: you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation, either version 3 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
- */
-/*
- * ============================================================================
- *
- * Filename: testdata.h
- *
- * Description: Data for tests
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#ifndef TESTDATA_H
-#define TESTDATA_H
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <strings.h>
-#include <errno.h>
-#include <stdint.h>
-#include <time.h>
-#ifndef _WIN32
-#include <unistd.h>
-#endif
-#include <sys/stat.h>
-#include <sys/types.h>
-
-/* TinyTest */
-#include "tinytest.h"
-#include "tinytest_macros.h"
-#include "testdata.h"
-#include "helpers.h"
-
-
-extern const size_t n_loremipsum_lines;
-extern const size_t loremipsum_fsize;
-extern const size_t loremipsum_line_lens[];
-extern const char *loremipsum_lines[];
-extern const char *first_fastq_read[];
-extern const size_t first_fastq_len;
-extern struct testcase_t data_tests[];
-extern const size_t n_codons;
-extern const char *codon_list[];
-extern const char aa_list[];
-
-void test_data_files (void *ptr);
-
-#endif /* TESTDATA_H */
diff --git a/src/libqes/test/tests.h b/src/libqes/test/tests.h
deleted file mode 100644
index 3d3eafa..0000000
--- a/src/libqes/test/tests.h
+++ /dev/null
@@ -1,57 +0,0 @@
-/*
- * ============================================================================
- *
- * Filename: tests.h
- *
- * Description: Tests for libqes
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#ifndef TESTS_H
-#define TESTS_H
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <strings.h>
-#include <errno.h>
-#include <stdint.h>
-#include <time.h>
-#ifndef _WIN32
-#include <unistd.h>
-#endif
-#include <sys/stat.h>
-#include <sys/types.h>
-
-/* TinyTest */
-#include "tinytest.h"
-#include "tinytest_macros.h"
-#include "testdata.h"
-#include "helpers.h"
-
-#define QES_DEFAULT_ERR_FN errnil
-#define QES_EXIT_FN (void)
-#include <qes_util.h>
-
-
-/* test_util tests */
-extern struct testcase_t qes_util_tests[];
-/* test_match tests */
-extern struct testcase_t qes_match_tests[];
-/* test_qes_file tests */
-extern struct testcase_t qes_file_tests[];
-/* test_seqfile tests */
-extern struct testcase_t qes_seqfile_tests[];
-/* test_seq tests */
-extern struct testcase_t qes_seq_tests[];
-/* test_sequtil tests */
-extern struct testcase_t qes_sequtil_tests[];
-/* test_log tests */
-extern struct testcase_t qes_log_tests[];
-/* test_helpers tests */
-extern struct testcase_t helper_tests[];
-
-#endif /* TESTS_H */
diff --git a/src/libqes/test/tinytest/tinytest.c b/src/libqes/test/tinytest/tinytest.c
deleted file mode 100644
index 3a8e331..0000000
--- a/src/libqes/test/tinytest/tinytest.c
+++ /dev/null
@@ -1,493 +0,0 @@
-/* tinytest.c -- Copyright 2009-2012 Nick Mathewson
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- * 1. Redistributions of source code must retain the above copyright
- * notice, this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright
- * notice, this list of conditions and the following disclaimer in the
- * documentation and/or other materials provided with the distribution.
- * 3. The name of the author may not be used to endorse or promote products
- * derived from this software without specific prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
- * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
- * IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
- * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
- * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
- * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
- * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
- * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-#ifdef TINYTEST_LOCAL
-#include "tinytest_local.h"
-#endif
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <assert.h>
-
-#ifndef NO_FORKING
-
-#ifdef _WIN32
-#include <windows.h>
-#else
-#include <sys/types.h>
-#include <sys/wait.h>
-#include <unistd.h>
-#endif
-
-#if defined(__APPLE__) && defined(__ENVIRONMENT_MAC_OS_X_VERSION_MIN_REQUIRED__)
-#if (__ENVIRONMENT_MAC_OS_X_VERSION_MIN_REQUIRED__ >= 1060 && \
- __ENVIRONMENT_MAC_OS_X_VERSION_MIN_REQUIRED__ < 1070)
-/* Workaround for a stupid bug in OSX 10.6 */
-#define FORK_BREAKS_GCOV
-#include <vproc.h>
-#endif
-#endif
-
-#endif /* !NO_FORKING */
-
-#ifndef __GNUC__
-#define __attribute__(x)
-#endif
-
-#include "tinytest.h"
-#include "tinytest_macros.h"
-
-#define LONGEST_TEST_NAME 16384
-
-static int in_tinytest_main = 0; /**< true if we're in tinytest_main().*/
-static int n_ok = 0; /**< Number of tests that have passed */
-static int n_bad = 0; /**< Number of tests that have failed. */
-static int n_skipped = 0; /**< Number of tests that have been skipped. */
-
-static int opt_forked = 0; /**< True iff we're called from inside a win32 fork*/
-static int opt_nofork = 0; /**< Suppress calls to fork() for debugging. */
-static int opt_verbosity = 1; /**< -==quiet,0==terse,1==normal,2==verbose */
-const char *verbosity_flag = "";
-
-const struct testlist_alias_t *cfg_aliases=NULL;
-
-enum outcome { SKIP=2, OK=1, FAIL=0 };
-static enum outcome cur_test_outcome = 0;
-const char *cur_test_prefix = NULL; /**< prefix of the current test group */
-/** Name of the current test, if we haven't logged is yet. Used for --quiet */
-const char *cur_test_name = NULL;
-
-#ifdef _WIN32
-/* Copy of argv[0] for win32. */
-static char commandname[MAX_PATH+1];
-#endif
-
-static void usage(struct testgroup_t *groups, int list_groups)
- __attribute__((noreturn));
-static int process_test_option(struct testgroup_t *groups, const char *test);
-
-static enum outcome
-testcase_run_bare_(const struct testcase_t *testcase)
-{
- void *env = NULL;
- int outcome;
- if (testcase->setup) {
- env = testcase->setup->setup_fn(testcase);
- if (!env)
- return FAIL;
- else if (env == (void*)TT_SKIP)
- return SKIP;
- }
-
- cur_test_outcome = OK;
- testcase->fn(env);
- outcome = cur_test_outcome;
-
- if (testcase->setup) {
- if (testcase->setup->cleanup_fn(testcase, env) == 0)
- outcome = FAIL;
- }
-
- return outcome;
-}
-
-#define MAGIC_EXITCODE 42
-
-#ifndef NO_FORKING
-
-static enum outcome
-testcase_run_forked_(const struct testgroup_t *group,
- const struct testcase_t *testcase)
-{
-#ifdef _WIN32
- /* Fork? On Win32? How primitive! We'll do what the smart kids do:
- we'll invoke our own exe (whose name we recall from the command
- line) with a command line that tells it to run just the test we
- want, and this time without forking.
-
- (No, threads aren't an option. The whole point of forking is to
- share no state between tests.)
- */
- int ok;
- char buffer[LONGEST_TEST_NAME+256];
- STARTUPINFOA si;
- PROCESS_INFORMATION info;
- DWORD exitcode;
-
- if (!in_tinytest_main) {
- printf("\nERROR. On Windows, testcase_run_forked_ must be"
- " called from within tinytest_main.\n");
- abort();
- }
- if (opt_verbosity>0)
- printf("[forking] ");
-
- snprintf(buffer, sizeof(buffer), "%s --RUNNING-FORKED %s %s%s",
- commandname, verbosity_flag, group->prefix, testcase->name);
-
- memset(&si, 0, sizeof(si));
- memset(&info, 0, sizeof(info));
- si.cb = sizeof(si);
-
- ok = CreateProcessA(commandname, buffer, NULL, NULL, 0,
- 0, NULL, NULL, &si, &info);
- if (!ok) {
- printf("CreateProcess failed!\n");
- return 0;
- }
- WaitForSingleObject(info.hProcess, INFINITE);
- GetExitCodeProcess(info.hProcess, &exitcode);
- CloseHandle(info.hProcess);
- CloseHandle(info.hThread);
- if (exitcode == 0)
- return OK;
- else if (exitcode == MAGIC_EXITCODE)
- return SKIP;
- else
- return FAIL;
-#else
- int outcome_pipe[2];
- pid_t pid;
- (void)group;
-
- if (pipe(outcome_pipe))
- perror("opening pipe");
-
- if (opt_verbosity>0)
- printf("[forking] ");
- pid = fork();
-#ifdef FORK_BREAKS_GCOV
- vproc_transaction_begin(0);
-#endif
- if (!pid) {
- /* child. */
- int test_r, write_r;
- char b[1];
- close(outcome_pipe[0]);
- test_r = testcase_run_bare_(testcase);
- assert(0<=(int)test_r && (int)test_r<=2);
- b[0] = "NYS"[test_r];
- write_r = (int)write(outcome_pipe[1], b, 1);
- if (write_r != 1) {
- perror("write outcome to pipe");
- exit(1);
- }
- exit(0);
- return FAIL; /* unreachable */
- } else {
- /* parent */
- int status, r;
- char b[1];
- /* Close this now, so that if the other side closes it,
- * our read fails. */
- close(outcome_pipe[1]);
- r = (int)read(outcome_pipe[0], b, 1);
- if (r == 0) {
- printf("[Lost connection!] ");
- return 0;
- } else if (r != 1) {
- perror("read outcome from pipe");
- }
- waitpid(pid, &status, 0);
- close(outcome_pipe[0]);
- return b[0]=='Y' ? OK : (b[0]=='S' ? SKIP : FAIL);
- }
-#endif
-}
-
-#endif /* !NO_FORKING */
-
-int
-testcase_run_one(const struct testgroup_t *group,
- const struct testcase_t *testcase)
-{
- enum outcome outcome;
-
- if (testcase->flags & (TT_SKIP|TT_OFF_BY_DEFAULT)) {
- if (opt_verbosity>0)
- printf("%s%s: %s\n",
- group->prefix, testcase->name,
- (testcase->flags & TT_SKIP) ? "SKIPPED" : "DISABLED");
- ++n_skipped;
- return SKIP;
- }
-
- if (opt_verbosity>0 && !opt_forked) {
- printf("%s%s: ", group->prefix, testcase->name);
- } else {
- if (opt_verbosity==0) printf(".");
- cur_test_prefix = group->prefix;
- cur_test_name = testcase->name;
- }
-
-#ifndef NO_FORKING
- if ((testcase->flags & TT_FORK) && !(opt_forked||opt_nofork)) {
- outcome = testcase_run_forked_(group, testcase);
- } else {
-#else
- {
-#endif
- outcome = testcase_run_bare_(testcase);
- }
-
- if (outcome == OK) {
- ++n_ok;
- if (opt_verbosity>0 && !opt_forked)
- puts(opt_verbosity==1?"OK":"");
- } else if (outcome == SKIP) {
- ++n_skipped;
- if (opt_verbosity>0 && !opt_forked)
- puts("SKIPPED");
- } else {
- ++n_bad;
- if (!opt_forked)
- printf("\n [%s FAILED]\n", testcase->name);
- }
-
- if (opt_forked) {
- exit(outcome==OK ? 0 : (outcome==SKIP?MAGIC_EXITCODE : 1));
- return 1; /* unreachable */
- } else {
- return (int)outcome;
- }
-}
-
-int
-tinytest_set_flag_(struct testgroup_t *groups, const char *arg, int set, unsigned long flag)
-{
- int i, j;
- size_t length = LONGEST_TEST_NAME;
- char fullname[LONGEST_TEST_NAME];
- int found=0;
- if (strstr(arg, ".."))
- length = strstr(arg,"..")-arg;
- for (i=0; groups[i].prefix; ++i) {
- for (j=0; groups[i].cases[j].name; ++j) {
- struct testcase_t *testcase = &groups[i].cases[j];
- snprintf(fullname, sizeof(fullname), "%s%s",
- groups[i].prefix, testcase->name);
- if (!flag) { /* Hack! */
- printf(" %s", fullname);
- if (testcase->flags & TT_OFF_BY_DEFAULT)
- puts(" (Off by default)");
- else if (testcase->flags & TT_SKIP)
- puts(" (DISABLED)");
- else
- puts("");
- }
- if (!strncmp(fullname, arg, length)) {
- if (set)
- testcase->flags |= flag;
- else
- testcase->flags &= ~flag;
- ++found;
- }
- }
- }
- return found;
-}
-
-static void
-usage(struct testgroup_t *groups, int list_groups)
-{
- puts("Options are: [--verbose|--quiet|--terse] [--no-fork]");
- puts(" Specify tests by name, or using a prefix ending with '..'");
- puts(" To skip a test, prefix its name with a colon.");
- puts(" To enable a disabled test, prefix its name with a plus.");
- puts(" Use --list-tests for a list of tests.");
- if (list_groups) {
- puts("Known tests are:");
- tinytest_set_flag_(groups, "..", 1, 0);
- }
- exit(0);
-}
-
-static int
-process_test_alias(struct testgroup_t *groups, const char *test)
-{
- int i, j, n, r;
- for (i=0; cfg_aliases && cfg_aliases[i].name; ++i) {
- if (!strcmp(cfg_aliases[i].name, test)) {
- n = 0;
- for (j = 0; cfg_aliases[i].tests[j]; ++j) {
- r = process_test_option(groups, cfg_aliases[i].tests[j]);
- if (r<0)
- return -1;
- n += r;
- }
- return n;
- }
- }
- printf("No such test alias as @%s!",test);
- return -1;
-}
-
-static int
-process_test_option(struct testgroup_t *groups, const char *test)
-{
- int flag = TT_ENABLED_;
- int n = 0;
- if (test[0] == '@') {
- return process_test_alias(groups, test + 1);
- } else if (test[0] == ':') {
- ++test;
- flag = TT_SKIP;
- } else if (test[0] == '+') {
- ++test;
- ++n;
- if (!tinytest_set_flag_(groups, test, 0, TT_OFF_BY_DEFAULT)) {
- printf("No such test as %s!\n", test);
- return -1;
- }
- } else {
- ++n;
- }
- if (!tinytest_set_flag_(groups, test, 1, flag)) {
- printf("No such test as %s!\n", test);
- return -1;
- }
- return n;
-}
-
-void
-tinytest_set_aliases(const struct testlist_alias_t *aliases)
-{
- cfg_aliases = aliases;
-}
-
-int
-tinytest_main(int c, const char **v, struct testgroup_t *groups)
-{
- int i, j, n=0;
-
-#ifdef _WIN32
- const char *sp = strrchr(v[0], '.');
- const char *extension = "";
- if (!sp || stricmp(sp, ".exe"))
- extension = ".exe"; /* Add an exe so CreateProcess will work */
- snprintf(commandname, sizeof(commandname), "%s%s", v[0], extension);
- commandname[MAX_PATH]='\0';
-#endif
- for (i=1; i<c; ++i) {
- if (v[i][0] == '-') {
- if (!strcmp(v[i], "--RUNNING-FORKED")) {
- opt_forked = 1;
- } else if (!strcmp(v[i], "--no-fork")) {
- opt_nofork = 1;
- } else if (!strcmp(v[i], "--quiet")) {
- opt_verbosity = -1;
- verbosity_flag = "--quiet";
- } else if (!strcmp(v[i], "--verbose")) {
- opt_verbosity = 2;
- verbosity_flag = "--verbose";
- } else if (!strcmp(v[i], "--terse")) {
- opt_verbosity = 0;
- verbosity_flag = "--terse";
- } else if (!strcmp(v[i], "--help")) {
- usage(groups, 0);
- } else if (!strcmp(v[i], "--list-tests")) {
- usage(groups, 1);
- } else {
- printf("Unknown option %s. Try --help\n",v[i]);
- return -1;
- }
- } else {
- int r = process_test_option(groups, v[i]);
- if (r<0)
- return -1;
- n += r;
- }
- }
- if (!n)
- tinytest_set_flag_(groups, "..", 1, TT_ENABLED_);
-
-#ifdef _IONBF
- setvbuf(stdout, NULL, _IONBF, 0);
-#endif
-
- ++in_tinytest_main;
- for (i=0; groups[i].prefix; ++i)
- for (j=0; groups[i].cases[j].name; ++j)
- if (groups[i].cases[j].flags & TT_ENABLED_)
- testcase_run_one(&groups[i],
- &groups[i].cases[j]);
-
- --in_tinytest_main;
-
- if (opt_verbosity==0)
- puts("");
-
- if (n_bad)
- printf("%d/%d TESTS FAILED. (%d skipped)\n", n_bad,
- n_bad+n_ok,n_skipped);
- else if (opt_verbosity >= 1)
- printf("%d tests ok. (%d skipped)\n", n_ok, n_skipped);
-
- return (n_bad == 0) ? 0 : 1;
-}
-
-int
-tinytest_get_verbosity_(void)
-{
- return opt_verbosity;
-}
-
-void
-tinytest_set_test_failed_(void)
-{
- if (opt_verbosity <= 0 && cur_test_name) {
- if (opt_verbosity==0) puts("");
- printf("%s%s: ", cur_test_prefix, cur_test_name);
- cur_test_name = NULL;
- }
- cur_test_outcome = 0;
-}
-
-void
-tinytest_set_test_skipped_(void)
-{
- if (cur_test_outcome==OK)
- cur_test_outcome = SKIP;
-}
-
-char *
-tinytest_format_hex_(const void *val_, unsigned long len)
-{
- const unsigned char *val = val_;
- char *result, *cp;
- size_t i;
-
- if (!val)
- return strdup("null");
- if (!(result = malloc(len*2+1)))
- return strdup("<allocation failure>");
- cp = result;
- for (i=0;i<len;++i) {
- *cp++ = "0123456789ABCDEF"[val[i] >> 4];
- *cp++ = "0123456789ABCDEF"[val[i] & 0x0f];
- }
- *cp = 0;
- return result;
-}
diff --git a/src/libqes/test/tinytest/tinytest.h b/src/libqes/test/tinytest/tinytest.h
deleted file mode 100644
index ed07b26..0000000
--- a/src/libqes/test/tinytest/tinytest.h
+++ /dev/null
@@ -1,100 +0,0 @@
-/* tinytest.h -- Copyright 2009-2012 Nick Mathewson
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- * 1. Redistributions of source code must retain the above copyright
- * notice, this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright
- * notice, this list of conditions and the following disclaimer in the
- * documentation and/or other materials provided with the distribution.
- * 3. The name of the author may not be used to endorse or promote products
- * derived from this software without specific prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
- * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
- * IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
- * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
- * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
- * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
- * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
- * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-
-#ifndef TINYTEST_H_INCLUDED_
-#define TINYTEST_H_INCLUDED_
-
-/** Flag for a test that needs to run in a subprocess. */
-#define TT_FORK (1<<0)
-/** Runtime flag for a test we've decided to skip. */
-#define TT_SKIP (1<<1)
-/** Internal runtime flag for a test we've decided to run. */
-#define TT_ENABLED_ (1<<2)
-/** Flag for a test that's off by default. */
-#define TT_OFF_BY_DEFAULT (1<<3)
-/** If you add your own flags, make them start at this point. */
-#define TT_FIRST_USER_FLAG (1<<4)
-
-typedef void (*testcase_fn)(void *);
-
-struct testcase_t;
-
-/** Functions to initialize/teardown a structure for a testcase. */
-struct testcase_setup_t {
- /** Return a new structure for use by a given testcase. */
- void *(*setup_fn)(const struct testcase_t *);
- /** Clean/free a structure from setup_fn. Return 1 if ok, 0 on err. */
- int (*cleanup_fn)(const struct testcase_t *, void *);
-};
-
-/** A single test-case that you can run. */
-struct testcase_t {
- const char *name; /**< An identifier for this case. */
- testcase_fn fn; /**< The function to run to implement this case. */
- unsigned long flags; /**< Bitfield of TT_* flags. */
- const struct testcase_setup_t *setup; /**< Optional setup/cleanup fns*/
- void *setup_data; /**< Extra data usable by setup function */
-};
-#define END_OF_TESTCASES { NULL, NULL, 0, NULL, NULL }
-
-/** A group of tests that are selectable together. */
-struct testgroup_t {
- const char *prefix; /**< Prefix to prepend to testnames. */
- struct testcase_t *cases; /** Array, ending with END_OF_TESTCASES */
-};
-#define END_OF_GROUPS { NULL, NULL}
-
-struct testlist_alias_t {
- const char *name;
- const char **tests;
-};
-#define END_OF_ALIASES { NULL, NULL }
-
-/** Implementation: called from a test to indicate failure, before logging. */
-void tinytest_set_test_failed_(void);
-/** Implementation: called from a test to indicate that we're skipping. */
-void tinytest_set_test_skipped_(void);
-/** Implementation: return 0 for quiet, 1 for normal, 2 for loud. */
-int tinytest_get_verbosity_(void);
-/** Implementation: Set a flag on tests matching a name; returns number
- * of tests that matched. */
-int tinytest_set_flag_(struct testgroup_t *, const char *, int set, unsigned long);
-/** Implementation: Put a chunk of memory into hex. */
-char *tinytest_format_hex_(const void *, unsigned long);
-
-/** Set all tests in 'groups' matching the name 'named' to be skipped. */
-#define tinytest_skip(groups, named) \
- tinytest_set_flag_(groups, named, 1, TT_SKIP)
-
-/** Run a single testcase in a single group. */
-int testcase_run_one(const struct testgroup_t *,const struct testcase_t *);
-
-void tinytest_set_aliases(const struct testlist_alias_t *aliases);
-
-/** Run a set of testcases from an END_OF_GROUPS-terminated array of groups,
- as selected from the command line. */
-int tinytest_main(int argc, const char **argv, struct testgroup_t *groups);
-
-#endif
diff --git a/src/libqes/test/tinytest/tinytest_macros.h b/src/libqes/test/tinytest/tinytest_macros.h
deleted file mode 100644
index c3728d1..0000000
--- a/src/libqes/test/tinytest/tinytest_macros.h
+++ /dev/null
@@ -1,199 +0,0 @@
-/* tinytest_macros.h -- Copyright 2009-2012 Nick Mathewson
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- * 1. Redistributions of source code must retain the above copyright
- * notice, this list of conditions and the following disclaimer.
- * 2. Redistributions in binary form must reproduce the above copyright
- * notice, this list of conditions and the following disclaimer in the
- * documentation and/or other materials provided with the distribution.
- * 3. The name of the author may not be used to endorse or promote products
- * derived from this software without specific prior written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
- * IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
- * OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
- * IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT,
- * INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
- * NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
- * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
- * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF
- * THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- */
-
-#ifndef TINYTEST_MACROS_H_INCLUDED_
-#define TINYTEST_MACROS_H_INCLUDED_
-
-/* Helpers for defining statement-like macros */
-#define TT_STMT_BEGIN do {
-#define TT_STMT_END } while (0)
-
-/* Redefine this if your test functions want to abort with something besides
- * "goto end;" */
-#ifndef TT_EXIT_TEST_FUNCTION
-#define TT_EXIT_TEST_FUNCTION TT_STMT_BEGIN goto end; TT_STMT_END
-#endif
-
-/* Redefine this if you want to note success/failure in some different way. */
-#ifndef TT_DECLARE
-#define TT_DECLARE(prefix, args) \
- TT_STMT_BEGIN \
- printf("\n %s %s:%d: ",prefix,__FILE__,__LINE__); \
- printf args ; \
- TT_STMT_END
-#endif
-
-/* Announce a failure. Args are parenthesized printf args. */
-#define TT_GRIPE(args) TT_DECLARE("FAIL", args)
-
-/* Announce a non-failure if we're verbose. */
-#define TT_BLATHER(args) \
- TT_STMT_BEGIN \
- if (tinytest_get_verbosity_()>1) TT_DECLARE(" OK", args); \
- TT_STMT_END
-
-#define TT_DIE(args) \
- TT_STMT_BEGIN \
- tinytest_set_test_failed_(); \
- TT_GRIPE(args); \
- TT_EXIT_TEST_FUNCTION; \
- TT_STMT_END
-
-#define TT_FAIL(args) \
- TT_STMT_BEGIN \
- tinytest_set_test_failed_(); \
- TT_GRIPE(args); \
- TT_STMT_END
-
-/* Fail and abort the current test for the reason in msg */
-#define tt_abort_printf(msg) TT_DIE(msg)
-#define tt_abort_perror(op) TT_DIE(("%s: %s [%d]",(op),strerror(errno), errno))
-#define tt_abort_msg(msg) TT_DIE(("%s", msg))
-#define tt_abort() TT_DIE(("%s", "(Failed.)"))
-
-/* Fail but do not abort the current test for the reason in msg. */
-#define tt_failprint_f(msg) TT_FAIL(msg)
-#define tt_fail_perror(op) TT_FAIL(("%s: %s [%d]",(op),strerror(errno), errno))
-#define tt_fail_msg(msg) TT_FAIL(("%s", msg))
-#define tt_fail() TT_FAIL(("%s", "(Failed.)"))
-
-/* End the current test, and indicate we are skipping it. */
-#define tt_skip() \
- TT_STMT_BEGIN \
- tinytest_set_test_skipped_(); \
- TT_EXIT_TEST_FUNCTION; \
- TT_STMT_END
-
-#define tt_want_(b, msg, fail) \
- TT_STMT_BEGIN \
- if (!(b)) { \
- tinytest_set_test_failed_(); \
- TT_GRIPE(("%s",msg)); \
- fail; \
- } else { \
- TT_BLATHER(("%s",msg)); \
- } \
- TT_STMT_END
-
-/* Assert b, but do not stop the test if b fails. Log msg on failure. */
-#define tt_want_msg(b, msg) \
- tt_want_(b, msg, );
-
-/* Assert b and stop the test if b fails. Log msg on failure. */
-#define tt_assert_msg(b, msg) \
- tt_want_(b, msg, TT_EXIT_TEST_FUNCTION);
-
-/* Assert b, but do not stop the test if b fails. */
-#define tt_want(b) tt_want_msg( (b), "want("#b")")
-/* Assert b, and stop the test if b fails. */
-#define tt_assert(b) tt_assert_msg((b), "assert("#b")")
-
-#define tt_assert_test_fmt_type(a,b,str_test,type,test,printf_type,printf_fmt, \
- setup_block,cleanup_block,die_on_fail) \
- TT_STMT_BEGIN \
- type val1_ = (a); \
- type val2_ = (b); \
- int tt_status_ = (test); \
- if (!tt_status_ || tinytest_get_verbosity_()>1) { \
- printf_type print_; \
- printf_type print1_; \
- printf_type print2_; \
- type value_ = val1_; \
- setup_block; \
- print1_ = print_; \
- value_ = val2_; \
- setup_block; \
- print2_ = print_; \
- TT_DECLARE(tt_status_?" OK":"FAIL", \
- ("assert(%s): "printf_fmt" vs "printf_fmt, \
- str_test, print1_, print2_)); \
- print_ = print1_; \
- cleanup_block; \
- print_ = print2_; \
- cleanup_block; \
- if (!tt_status_) { \
- tinytest_set_test_failed_(); \
- die_on_fail ; \
- } \
- } \
- TT_STMT_END
-
-#define tt_assert_test_type(a,b,str_test,type,test,fmt,die_on_fail) \
- tt_assert_test_fmt_type(a,b,str_test,type,test,type,fmt, \
- {print_=value_;},{},die_on_fail)
-
-#define tt_assert_test_type_opt(a,b,str_test,type,test,fmt,die_on_fail) \
- tt_assert_test_fmt_type(a,b,str_test,type,test,type,fmt, \
- {print_=value_?value_:"<NULL>";},{},die_on_fail)
-
-/* Helper: assert that a op b, when cast to type. Format the values with
- * printf format fmt on failure. */
-#define tt_assert_op_type(a,op,b,type,fmt) \
- tt_assert_test_type(a,b,#a" "#op" "#b,type,(val1_ op val2_),fmt, \
- TT_EXIT_TEST_FUNCTION)
-
-#define tt_int_op(a,op,b) \
- tt_assert_test_type(a,b,#a" "#op" "#b,long,(val1_ op val2_), \
- "%ld",TT_EXIT_TEST_FUNCTION)
-
-#define tt_uint_op(a,op,b) \
- tt_assert_test_type(a,b,#a" "#op" "#b,unsigned long, \
- (val1_ op val2_),"%lu",TT_EXIT_TEST_FUNCTION)
-
-#define tt_ptr_op(a,op,b) \
- tt_assert_test_type(a,b,#a" "#op" "#b,const void*, \
- (val1_ op val2_),"%p",TT_EXIT_TEST_FUNCTION)
-
-#define tt_str_op(a,op,b) \
- tt_assert_test_type_opt(a,b,#a" "#op" "#b,const char *, \
- (val1_ && val2_ && strcmp(val1_,val2_) op 0),"<%s>", \
- TT_EXIT_TEST_FUNCTION)
-
-#define tt_mem_op(expr1, op, expr2, len) \
- tt_assert_test_fmt_type(expr1,expr2,#expr1" "#op" "#expr2, \
- const void *, \
- (val1_ && val2_ && memcmp(val1_, val2_, len) op 0), \
- char *, "%s", \
- { print_ = tinytest_format_hex_(value_, (len)); }, \
- { if (print_) free(print_); }, \
- TT_EXIT_TEST_FUNCTION \
- );
-
-#define tt_want_int_op(a,op,b) \
- tt_assert_test_type(a,b,#a" "#op" "#b,long,(val1_ op val2_),"%ld",(void)0)
-
-#define tt_want_uint_op(a,op,b) \
- tt_assert_test_type(a,b,#a" "#op" "#b,unsigned long, \
- (val1_ op val2_),"%lu",(void)0)
-
-#define tt_want_ptr_op(a,op,b) \
- tt_assert_test_type(a,b,#a" "#op" "#b,const void*, \
- (val1_ op val2_),"%p",(void)0)
-
-#define tt_want_str_op(a,op,b) \
- tt_assert_test_type(a,b,#a" "#op" "#b,const char *, \
- (strcmp(val1_,val2_) op 0),"<%s>",(void)0)
-
-#endif
diff --git a/src/libqes/util/make_codon_list.py b/src/libqes/util/make_codon_list.py
deleted file mode 100644
index 0611413..0000000
--- a/src/libqes/util/make_codon_list.py
+++ /dev/null
@@ -1,38 +0,0 @@
-from Bio.Data import CodonTable
-
-nts = "ACGTU"
-codons = []
-aas = []
-codon_tab = CodonTable.generic_by_name["Standard"].forward_table
-for a in nts:
- for b in nts:
- for c in nts:
- codon = "".join((a,b,c))
- try:
- aa = codon_tab[codon.replace("U", "T")]
- except KeyError:
- aa = "*"
- codons.append(codon)
- aas.append(aa)
-n = 0
-print "const size_t n_codons = %s;" % len(codons)
-print
-print "const char *codon_list[] = {" ,
-for cdn in codons:
- if n % 5 == 0:
- print "\n ",
- print '"%s", ' % cdn,
- n += 1
-print
-print "};"
-n = 0
-print
-print "const char aa_list[] = {",
-for aa in aas:
- if n % 5 == 0:
- print "\n ",
- print "'%s', " % aa,
- n += 1
-print
-print "};"
-print
diff --git a/src/libqes/util/make_codon_map.py b/src/libqes/util/make_codon_map.py
deleted file mode 100644
index d300dd8..0000000
--- a/src/libqes/util/make_codon_map.py
+++ /dev/null
@@ -1,21 +0,0 @@
-from Bio.Data import CodonTable
-
-nts = "ACGTU"
-
-codon_tab = CodonTable.generic_by_name["Standard"].forward_table
-print "char\ntranslate_codon(char *codon)\n{"
-for a in nts:
- print " else if (codon[0] == '%s') {" % a
- for b in nts:
- print " else if (codon[1] == '%s') {" % b
- for c in nts:
- print " else if (codon[2] == '%s')" % c ,
- codon = "".join((a,b,c))
- try:
- aa = codon_tab[codon]
- except KeyError:
- aa = "*"
- print "return '%s'" % aa
- print " }"
- print " }"
-print "}"
--
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