[med-svn] [axe-demultiplexer] 01/04: Imported Upstream version 0.3.0+dfsg
Kevin Murray
daube-guest at moszumanska.debian.org
Tue Oct 27 22:06:23 UTC 2015
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a commit to branch master
in repository axe-demultiplexer.
commit 5fd41eb738307ef8cf8da359e352fb40b5c1f3f0
Author: Kevin Murray <spam at kdmurray.id.au>
Date: Wed Oct 21 15:55:55 2015 +1100
Imported Upstream version 0.3.0+dfsg
---
.gitattributes | 1 +
.gitignore | 1 +
.gitmodules | 3 +
.travis.yml | 44 +-
CMakeLists.txt | 10 +-
README.md | 10 +-
docs/CMakeLists.txt | 2 +
docs/conf.py | 7 +-
docs/gitversion.py | 189 +
docs/usage.rst | 9 +-
docs/usage.txt | 6 +-
src/CMakeLists.txt | 30 +-
src/axe.c | 20 +-
src/axe.h | 31 +-
src/axe_config.h.in | 18 +-
src/gsl/combination.c | 171 -
src/gsl/error.c | 77 -
src/gsl/gsl_combination.h | 76 -
src/gsl/gsl_errno.h | 153 -
src/gsl/gsl_message.h | 79 -
src/gsl/init.c | 127 -
src/gsl/message.c | 37 -
src/gsl/stream.c | 65 -
src/gsl/strerror.c | 100 -
src/libqes/.gitignore | 12 -
src/libqes/.travis.yml | 38 -
src/libqes/AUTHORS | 1 -
src/libqes/CMakeLists.txt | 154 -
src/libqes/LICENSE | 619 ---
src/libqes/README.md | 31 -
src/libqes/cmake-modules/CodeCoverage.cmake | 158 -
src/libqes/cmake-modules/FindLIBQES.cmake | 83 -
.../cmake-modules/GetGitRevisionDescription.cmake | 130 -
.../GetGitRevisionDescription.cmake.in | 38 -
src/libqes/cmake-modules/GitSemVer.cmake | 27 -
src/libqes/src/CMakeLists.txt | 16 -
src/libqes/src/crc.c | 101 -
src/libqes/src/crc.h | 46 -
src/libqes/src/qes.h | 26 -
src/libqes/src/qes_compat.c | 66 -
src/libqes/src/qes_compat.h | 29 -
src/libqes/src/qes_config.h.in | 76 -
src/libqes/src/qes_file.c | 496 ---
src/libqes/src/qes_file.h | 213 -
src/libqes/src/qes_libgnu.c | 16 -
src/libqes/src/qes_libgnu.h | 28 -
src/libqes/src/qes_log.c | 251 --
src/libqes/src/qes_log.h | 150 -
src/libqes/src/qes_match.c | 83 -
src/libqes/src/qes_match.h | 50 -
src/libqes/src/qes_seq.c | 157 -
src/libqes/src/qes_seq.h | 187 -
src/libqes/src/qes_seqfile.c | 319 --
src/libqes/src/qes_seqfile.h | 224 --
src/libqes/src/qes_sequtil.c | 256 --
src/libqes/src/qes_sequtil.h | 23 -
src/libqes/src/qes_str.c | 36 -
src/libqes/src/qes_str.h | 135 -
src/libqes/src/qes_util.c | 59 -
src/libqes/src/qes_util.h | 236 --
src/libqes/test/CMakeLists.txt | 36 -
src/libqes/test/benchmarks.c | 295 --
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/log_test.txt | 2 -
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/helpers.c | 191 -
src/libqes/test/helpers.h | 40 -
src/libqes/test/kseq.h | 235 --
src/libqes/test/logdemo.c | 34 -
src/libqes/test/test.c | 64 -
src/libqes/test/test_file.c | 430 ---
src/libqes/test/test_helpers.c | 54 -
src/libqes/test/test_log.c | 173 -
src/libqes/test/test_match.c | 89 -
src/libqes/test/test_seq.c | 422 --
src/libqes/test/test_seqfile.c | 402 --
src/libqes/test/test_sequtil.c | 51 -
src/libqes/test/test_util.c | 145 -
src/libqes/test/testdata.c | 144 -
src/libqes/test/testdata.h | 49 -
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 -
src/main.c | 32 +-
tests/CMakeLists.txt | 4 +-
tests/{axe_integration.py => axe_cli_tests.py} | 23 +-
102 files changed, 363 insertions(+), 17391 deletions(-)
diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000..0dfaea1
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1 @@
+docs/gitversion.py export-subst
diff --git a/.gitignore b/.gitignore
index b383896..27bbfc8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,6 +5,7 @@
# compiled
build
+*.pyc
*.o
*.a
*.so
diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000..3c4636a
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "src/libqes"]
+ path = src/libqes
+ url = https://github.com/kdmurray91/libqes.git
diff --git a/.travis.yml b/.travis.yml
index cb215e3..82afcc5 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -9,31 +9,41 @@ compiler:
- clang
- gcc
-before_install:
- - sudo add-apt-repository --yes ppa:kalakris/cmake
- - sudo apt-get update -qq
- - sudo apt-get install --yes cmake
- - sudo apt-get update
- - sudo apt-get install lcov python-pip valgrind libgsl0-dev
- - mkdir zlib && cd zlib
- - wget http://zlib.net/zlib-1.2.8.tar.gz
- - tar xvxf zlib-1.2.8.tar.gz
- - cd zlib-1.2.8
- - ./configure
- - make
- - sudo make install
- - cd ../..
+sudo: false
+
+notifications:
+ email:
+ - spam at kdmurray.id.au
+
+addons:
+ apt:
+ sources:
+ - kalakris-cmake
+ packages:
+ - cmake
+ - lcov
+ - libgsl0-dev
+ - python
+ - python-sphinx
install:
+ - pushd $HOME
+ - wget http://zlib.net/zlib-1.2.8.tar.xz
+ - tar xvf zlib-1.2.8.tar.xz
+ - cd zlib-1.2.8
+ - ./configure --prefix=$HOME
+ - make
+ - make install
+ - popd
- git submodule update --init
- mkdir build
- mkdir target
- cd build
script:
- - cmake .. -DCMAKE_INSTALL_PREFIX=../target -DCMAKE_BUILD_TYPE=$BUILD_TYPE
+ - cmake .. -DCMAKE_INSTALL_PREFIX=../target -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DZLIB_ROOT=$HOME
- make
- - python ../tests/axe_integration.py .
+ - python ../tests/axe_cli_tests.py .
- ./bin/test_axe
- make install
- - test -f ../target/bin/axe
+ - test -f ../target/bin/axe-demux
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 75fd536..4d4e6cd 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -29,7 +29,15 @@ MESSAGE(STATUS "${CMAKE_BUILD_TYPE} build of axe version: ${AXE_VERSION}")
## Find Packages and Headers ##
###############################
-# Done by libqes' CML.txt
+FIND_PACKAGE(ZLIB 1.2.5 REQUIRED)
+
+FIND_PACKAGE(GSL)
+
+IF (GSL_FOUND)
+ SET(AXE_DEP_INCLUDES ${GSL_INCLUDE_DIRS})
+ SET(AXE_DEP_LIBS ${GSL_LIBRARIES})
+ENDIF()
+
##########################
## Set Compiler Options ##
diff --git a/README.md b/README.md
index 5a18c3c..2fd6cc8 100644
--- a/README.md
+++ b/README.md
@@ -21,11 +21,17 @@ spirit of "release early and often", here it is.
| Jenkins GNU/Linux | [](http://biojenkins.anu.edu.au/job/axe/) |
| ----------------- | --- |
-| Jenkins MinGW | [](http://biojenkins.anu.edu.au/job/axe-mingw/) |
-| TravisCI | [](https://travis-ci.org/kdmurray91/axe) |
+| TravisCI | [](https://travis-ci.org/kdmurray91/axe) |
| Test Coverage | [](https://coveralls.io/r/kdmurray91/axe?branch=master) |
| Coverity Scans | [](https://scan.coverity.com/projects/2666) |
+Important Note
+--------------
+
+**For arcane reasons, the name of the ``axe`` binary changed to ``axe-demux``
+with version 0.3.0. Apologies for the inconvenience, this was required to
+make ``axe`` installable in Debian and its derivatives. Command-line usage
+did not change.**
Installation:
-------------
diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
index 5d808f8..68ec92a 100644
--- a/docs/CMakeLists.txt
+++ b/docs/CMakeLists.txt
@@ -20,5 +20,7 @@ IF(SPHINXBUILD)
ADD_CUSTOM_TARGET(doc ALL DEPENDS doc_man doc_onehtml)
INSTALL(FILES ${CMAKE_BINARY_DIR}/doc/man/axe.1 DESTINATION "share/man/man1")
SET_DIRECTORY_PROPERTIES(PROPERTY ADDITIONAL_MAKE_CLEAN_FILES doc/)
+ELSE()
+ MESSAGE(WARNING "Cannot build documenation, sphinx isn't installed")
ENDIF()
diff --git a/docs/conf.py b/docs/conf.py
index b7aca36..e3898b9 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -18,7 +18,8 @@ import os
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
-#sys.path.insert(0, os.path.abspath('.'))
+sys.path.insert(0, os.path.abspath('.'))
+import gitversion
# -- General configuration ------------------------------------------------
@@ -55,9 +56,9 @@ copyright = u'2014, Kevin Murray'
# built documents.
#
# The short X.Y version.
-version = '0.0.1'
+version = gitversion.get_versions()['version']
# The full version, including alpha/beta/rc tags.
-release = '0.0.1'
+release = version
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
diff --git a/docs/gitversion.py b/docs/gitversion.py
new file mode 100644
index 0000000..727a640
--- /dev/null
+++ b/docs/gitversion.py
@@ -0,0 +1,189 @@
+# This file helps to compute a version number in source trees obtained from
+# git-archive tarball (such as those provided by githubs download-from-tag
+# feature). Distribution tarballs (built by setup.py sdist) and build
+# directories (produced by setup.py build) will contain a much shorter file
+# that just contains the computed version number.
+
+# This file is released into the public domain. Generated by
+# versioneer-0.13 (https://github.com/warner/python-versioneer)
+
+# these strings will be replaced by git during git-archive
+git_refnames = " (HEAD -> master, tag: 0.3.0)"
+git_full = "577fdab42d670dfb8682980b0887fc947e3884e1"
+
+# these strings are filled in when 'setup.py versioneer' creates _version.py
+tag_prefix = ""
+parentdir_prefix = ""
+versionfile_source = "docs/version.py"
+
+import errno
+import os
+import re
+import subprocess
+import sys
+
+def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False):
+ assert isinstance(commands, list)
+ p = None
+ for c in commands:
+ try:
+ # remember shell=False, so use git.cmd on windows, not just git
+ p = subprocess.Popen([c] + args, cwd=cwd, stdout=subprocess.PIPE,
+ stderr=(subprocess.PIPE if hide_stderr
+ else None))
+ break
+ except EnvironmentError:
+ e = sys.exc_info()[1]
+ if e.errno == errno.ENOENT:
+ continue
+ if verbose:
+ print("unable to run %s" % args[0])
+ print(e)
+ return None
+ else:
+ if verbose:
+ print("unable to find command, tried %s" % (commands,))
+ return None
+ stdout = p.communicate()[0].strip()
+ if sys.version >= '3':
+ stdout = stdout.decode()
+ if p.returncode != 0:
+ if verbose:
+ print("unable to run %s (error)" % args[0])
+ return None
+ return stdout
+
+
+def versions_from_parentdir(parentdir_prefix, root, verbose=False):
+ # Source tarballs conventionally unpack into a directory that includes
+ # both the project name and a version string.
+ dirname = os.path.basename(root)
+ if not dirname.startswith(parentdir_prefix):
+ if verbose:
+ print("guessing rootdir is '%s', but '%s' doesn't start with "
+ "prefix '%s'" % (root, dirname, parentdir_prefix))
+ return None
+ return {"version": dirname[len(parentdir_prefix):], "full": ""}
+
+
+def git_get_keywords(versionfile_abs):
+ # the code embedded in _version.py can just fetch the value of these
+ # keywords. When used from setup.py, we don't want to import _version.py,
+ # so we do it with a regexp instead. This function is not used from
+ # _version.py.
+ keywords = {}
+ try:
+ f = open(versionfile_abs, "r")
+ for line in f.readlines():
+ if line.strip().startswith("git_refnames ="):
+ mo = re.search(r'=\s*"(.*)"', line)
+ if mo:
+ keywords["refnames"] = mo.group(1)
+ if line.strip().startswith("git_full ="):
+ mo = re.search(r'=\s*"(.*)"', line)
+ if mo:
+ keywords["full"] = mo.group(1)
+ f.close()
+ except EnvironmentError:
+ pass
+ return keywords
+
+
+def git_versions_from_keywords(keywords, tag_prefix, verbose=False):
+ if not keywords:
+ return {} # keyword-finding function failed to find keywords
+ refnames = keywords["refnames"].strip()
+ if refnames.startswith("$Format"):
+ if verbose:
+ print("keywords are unexpanded, not using")
+ return {} # unexpanded, so not in an unpacked git-archive tarball
+ refs = set([r.strip() for r in refnames.strip("()").split(",")])
+ # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
+ # just "foo-1.0". If we see a "tag: " prefix, prefer those.
+ TAG = "tag: "
+ tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
+ if not tags:
+ # Either we're using git < 1.8.3, or there really are no tags. We use
+ # a heuristic: assume all version tags have a digit. The old git %d
+ # expansion behaves like git log --decorate=short and strips out the
+ # refs/heads/ and refs/tags/ prefixes that would let us distinguish
+ # between branches and tags. By ignoring refnames without digits, we
+ # filter out many common branch names like "release" and
+ # "stabilization", as well as "HEAD" and "master".
+ tags = set([r for r in refs if re.search(r'\d', r)])
+ if verbose:
+ print("discarding '%s', no digits" % ",".join(refs-tags))
+ if verbose:
+ print("likely tags: %s" % ",".join(sorted(tags)))
+ for ref in sorted(tags):
+ # sorting will prefer e.g. "2.0" over "2.0rc1"
+ if ref.startswith(tag_prefix):
+ r = ref[len(tag_prefix):]
+ if verbose:
+ print("picking %s" % r)
+ return {"version": r,
+ "full": keywords["full"].strip()}
+ # no suitable tags, so we use the full revision id
+ if verbose:
+ print("no suitable tags, using full revision id")
+ return {"version": keywords["full"].strip(),
+ "full": keywords["full"].strip()}
+
+
+def git_versions_from_vcs(tag_prefix, root, verbose=False):
+ # this runs 'git' from the root of the source tree. This only gets called
+ # if the git-archive 'subst' keywords were *not* expanded, and
+ # _version.py hasn't already been rewritten with a short version string,
+ # meaning we're inside a checked out source tree.
+
+ if not os.path.exists(os.path.join(root, ".git")):
+ if verbose:
+ print("no .git in %s" % root)
+ return {}
+
+ GITS = ["git"]
+ if sys.platform == "win32":
+ GITS = ["git.cmd", "git.exe"]
+ stdout = run_command(GITS, ["describe", "--tags", "--dirty", "--always"],
+ cwd=root)
+ if stdout is None:
+ return {}
+ if not stdout.startswith(tag_prefix):
+ if verbose:
+ fmt = "tag '%s' doesn't start with prefix '%s'"
+ print(fmt % (stdout, tag_prefix))
+ return {}
+ tag = stdout[len(tag_prefix):]
+ stdout = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
+ if stdout is None:
+ return {}
+ full = stdout.strip()
+ if tag.endswith("-dirty"):
+ full += "-dirty"
+ return {"version": tag, "full": full}
+
+
+def get_versions(default={"version": "unknown", "full": ""}, verbose=False):
+ # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have
+ # __file__, we can work backwards from there to the root. Some
+ # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which
+ # case we can only use expanded keywords.
+
+ keywords = {"refnames": git_refnames, "full": git_full}
+ ver = git_versions_from_keywords(keywords, tag_prefix, verbose)
+ if ver:
+ return ver
+
+ try:
+ root = os.path.realpath(__file__)
+ # versionfile_source is the relative path from the top of the source
+ # tree (where the .git directory might live) to this file. Invert
+ # this to find the root from __file__.
+ for i in range(len(versionfile_source.split('/'))):
+ root = os.path.dirname(root)
+ except NameError:
+ return default
+
+ return (git_versions_from_vcs(tag_prefix, root, verbose)
+ or versions_from_parentdir(parentdir_prefix, root, verbose)
+ or default)
diff --git a/docs/usage.rst b/docs/usage.rst
index 6eabfba..ade6ed5 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -2,13 +2,20 @@
Axe Usage
*********
+.. note::
+ For arcane reasons, the name of the ``axe`` binary changed to ``axe-demux``
+ with version 0.3.0. Apologies for the inconvenience, this was required to
+ make ``axe`` installable in Debian and its derivatives. Command-line usage
+ did not change.
+
Axe has several usage modes. The primary distinction is between the two
alternate barcoding schemes, single and combinatorial barcoding. Single barcode
matching is used when only the first read contains barcode sequences.
Combinatorial barcoding is used when both reads in a read pair contain
independent (typically different) barcode sequences.
-For concise reference, the command-line usage of ``axe`` is reproduced below:
+For concise reference, the command-line usage of ``axe-demux`` is reproduced
+below:
.. literalinclude:: usage.txt
diff --git a/docs/usage.txt b/docs/usage.txt
index 31b52fe..2ab701e 100644
--- a/docs/usage.txt
+++ b/docs/usage.txt
@@ -1,7 +1,7 @@
USAGE:
-axe [-mzc2pt] -b (-f [-r] | -i) (-F [-R] | -I)
-axe -h
-axe -v
+axe-demux [-mzc2pt] -b (-f [-r] | -i) (-F [-R] | -I)
+axe-demux -h
+axe-demux -v
OPTIONS:
-m, --mismatch Maximum hamming distance mismatch. [int, default 1]
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index c94d70b..bc989b5 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,13 +1,33 @@
+# Copyright 2014-2015 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/>.
+
# Axe library (libaxe.a)
FILE(GLOB DATRIE_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/datrie/*.c)
FILE(GLOB GSL_SRCS ${CMAKE_CURRENT_SOURCE_DIR}/gsl/*.c)
-SET(AXELIB_SRCS ${DATRIE_SRCS} ${GSL_SRCS} axe.c)
+SET(AXELIB_SRCS ${DATRIE_SRCS} axe.c)
+
+IF (NOT GSL_FOUND)
+ MESSAGE(STATUS "Using bundled GSL sources")
+ SET(AXELIB_SRCS ${AXELIB_SRCS} ${GSL_SRCS})
+ENDIF()
ADD_LIBRARY(axelib STATIC ${AXELIB_SRCS})
-TARGET_LINK_LIBRARIES(axelib qes_static)
+TARGET_LINK_LIBRARIES(axelib qes_static ${AXE_DEP_LIBS})
SET_TARGET_PROPERTIES(axelib PROPERTIES OUTPUT_NAME axe)
# Executable
-ADD_EXECUTABLE(axe main.c)
-TARGET_LINK_LIBRARIES(axe ${AXE_DEPENDS_LIBS} axelib)
-INSTALL(TARGETS axe DESTINATION "bin")
+ADD_EXECUTABLE(axe-demux main.c)
+TARGET_LINK_LIBRARIES(axe-demux ${AXE_DEPENDS_LIBS} axelib)
+INSTALL(TARGETS axe-demux DESTINATION "bin")
diff --git a/src/axe.c b/src/axe.c
index b91ed69..ffcd13b 100644
--- a/src/axe.c
+++ b/src/axe.c
@@ -2,16 +2,22 @@
* ============================================================================
*
* Filename: axe.c
- *
* Description: Demultiplex reads by 5' barcodes
+ * Copyright: 2014-2015 Kevin Murray <spam at kdmurray.id.au>
+ * License: GNU GPL v3+
+ *
+ * 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.
*
- * Version: 1.0
- * Created: 11/06/14 12:17:17
- * Revision: none
- * License: GPLv3+
- * Compiler: gcc, clang
+ * 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.
*
- * Author: Kevin Murray, spam at kdmurray.id.au
+ * You should have received a copy of the GNU General Public License along with
+ * this program. If not, see <http://www.gnu.org/licenses/>.
*
* ============================================================================
*/
diff --git a/src/axe.h b/src/axe.h
index 68f6fdd..e1fe5b9 100644
--- a/src/axe.h
+++ b/src/axe.h
@@ -2,19 +2,26 @@
* ============================================================================
*
* Filename: axe.h
- *
* Description: Demultiplex reads by 5' barcodes
+ * Copyright: 2014-2015 Kevin Murray <spam at kdmurray.id.au>
+ * License: GNU GPL v3+
+ *
+ * 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.
*
- * Version: 1.0
- * Created: 11/06/14 12:19:39
- * Revision: none
- * License: GPLv3+
- * Compiler: gcc, clang
+ * 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.
*
- * Author: Kevin Murray, spam at kdmurray.id.au
+ * You should have received a copy of the GNU General Public License along with
+ * this program. If not, see <http://www.gnu.org/licenses/>.
*
* ============================================================================
*/
+
#ifndef AXE_H
#define AXE_H
@@ -172,7 +179,7 @@ axe_output_ok(const struct axe_output *output)
/*=== FUNCTION ============================================================*
Name: axe_config_create
-Paramters: void
+Parameters: void
Description: Create a struct axe_config on the heap and initialise members
to empty/null values.
Returns: struct axe_config *: A valid, empty struct axe_config, or NULL
@@ -182,7 +189,7 @@ struct axe_config *axe_config_create(void);
/*=== FUNCTION ============================================================*
Name: axe_config_destroy
-Paramters: struct axe_config *: config struct on heap to destroy.
+Parameters: struct axe_config *: config struct on heap to destroy.
Description: Destroy a ``struct axe_config`` on the heap, and set its
pointer variable to NULL;
Returns: void
@@ -196,7 +203,7 @@ void axe_config_destroy_(struct axe_config *config);
/*=== FUNCTION ============================================================*
Name: axe_output_create
-Paramters: const char *fwd_fpath: Forwards/interleaved read filepath
+Parameters: const char *fwd_fpath: Forwards/interleaved read filepath
const char *rev_fpath: Reverse read filepath
enum read_mode mode: Output mode
const char *fp_mode: qes_fopen() mode specifier. See
@@ -210,7 +217,7 @@ struct axe_output *axe_output_create(const char *fwd_fpath,
/*=== FUNCTION ============================================================*
Name: axe_output_destroy
-Paramters: struct axe_output *: output struct on heap to destroy.
+Parameters: struct axe_output *: output struct on heap to destroy.
Description: Destroy a ``struct axe_output`` on the heap, and set its
pointer variable to NULL;
Returns: void
@@ -230,7 +237,7 @@ extern int axe_trie_add(struct axe_trie *trie, const char *str,
extern int axe_trie_delete(struct axe_trie *trie, const char *str);
/*=== FUNCTION ============================================================*
Name: axe_trie_destroy
-Paramters: struct axe_trie *: trie struct on heap to destroy.
+Parameters: struct axe_trie *: trie struct on heap to destroy.
Description: Destroy a ``struct axe_trie`` on the heap, and set its
pointer variable to NULL;
Returns: void
diff --git a/src/axe_config.h.in b/src/axe_config.h.in
index ed20167..c084105 100644
--- a/src/axe_config.h.in
+++ b/src/axe_config.h.in
@@ -2,14 +2,22 @@
* ============================================================================
*
* Filename: axe_config.h.in
+ * Description: Pull in build system definitions
+ * Copyright: 2014-2015 Kevin Murray <spam at kdmurray.id.au>
+ * License: GNU GPL v3+
*
- * Description: Define various things from CMake.
+ * 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.
*
- * Created: 15/09/14 14:09:59
- * License: GPLv3+
- * Compiler: gcc, clang
+ * 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.
*
- * Author: Kevin Murray, spam at kdmurray.id.au
+ * You should have received a copy of the GNU General Public License along with
+ * this program. If not, see <http://www.gnu.org/licenses/>.
*
* ============================================================================
*/
diff --git a/src/gsl/combination.c b/src/gsl/combination.c
deleted file mode 100644
index 6401c04..0000000
--- a/src/gsl/combination.c
+++ /dev/null
@@ -1,171 +0,0 @@
-/* combination/combination.c
- * based on permutation/permutation.c by Brian Gough
- *
- * Copyright (C) 2001 Szymon Jaroszewicz
- *
- * 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, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
- */
-
-#include "gsl_errno.h"
-#include "gsl_combination.h"
-
-size_t
-gsl_combination_n (const gsl_combination * c)
-{
- return c->n ;
-}
-
-size_t
-gsl_combination_k (const gsl_combination * c)
-{
- return c->k ;
-}
-
-size_t *
-gsl_combination_data (const gsl_combination * c)
-{
- return c->data ;
-}
-
-int
-gsl_combination_valid (gsl_combination * c)
-{
- const size_t n = c->n ;
- const size_t k = c->k ;
-
- size_t i, j ;
-
- if( k > n )
- {
- GSL_ERROR("combination has k greater than n", GSL_FAILURE) ;
- }
- for (i = 0; i < k; i++)
- {
- const size_t ci = c->data[i];
-
- if (ci >= n)
- {
- GSL_ERROR("combination index outside range", GSL_FAILURE) ;
- }
-
- for (j = 0; j < i; j++)
- {
- if (c->data[j] == ci)
- {
- GSL_ERROR("duplicate combination index", GSL_FAILURE) ;
- }
- if (c->data[j] > ci)
- {
- GSL_ERROR("combination indices not in increasing order",
- GSL_FAILURE) ;
- }
- }
- }
-
- return GSL_SUCCESS;
-}
-
-
-int
-gsl_combination_next (gsl_combination * c)
-{
- /* Replaces c with the next combination (in the standard lexicographical
- * ordering). Returns GSL_FAILURE if there is no next combination.
- */
- const size_t n = c->n;
- const size_t k = c->k;
- size_t *data = c->data;
- size_t i;
-
- if(k == 0)
- {
- return GSL_FAILURE;
- }
- i = k - 1;
-
- while(i > 0 && data[i] == n - k + i)
- {
- i--;
- }
- if(i == 0 && data[i] == n - k)
- {
- return GSL_FAILURE;
- }
- data[i]++;
- for(; i < k - 1; i++)
- {
- data[i + 1] = data[i] + 1;
- }
- return GSL_SUCCESS;
-}
-
-int
-gsl_combination_prev (gsl_combination * c)
-{
- /* Replaces c with the previous combination (in the standard
- * lexicographical ordering). Returns GSL_FAILURE if there is no
- * previous combination.
- */
- const size_t n = c->n;
- const size_t k = c->k;
- size_t *data = c->data;
- size_t i;
-
- if(k == 0)
- {
- return GSL_FAILURE;
- }
- i = k - 1;
-
- while(i > 0 && data[i] == data[i-1] + 1)
- {
- i--;
- }
- if(i == 0 && data[i] == 0)
- {
- return GSL_FAILURE;
- }
- data[i++]--;
- for(; i < k; i++)
- {
- data[i] = n - k + i;
- }
- return GSL_SUCCESS;
-}
-
-int
-gsl_combination_memcpy (gsl_combination * dest, const gsl_combination * src)
-{
- const size_t src_n = src->n;
- const size_t src_k = src->k;
- const size_t dest_n = dest->n;
- const size_t dest_k = dest->k;
-
- if (src_n != dest_n || src_k != dest_k)
- {
- GSL_ERROR ("combination lengths are not equal", GSL_EBADLEN);
- }
-
- {
- size_t j;
-
- for (j = 0; j < src_k; j++)
- {
- dest->data[j] = src->data[j];
- }
- }
-
- return GSL_SUCCESS;
-}
diff --git a/src/gsl/error.c b/src/gsl/error.c
deleted file mode 100644
index ef4a45e..0000000
--- a/src/gsl/error.c
+++ /dev/null
@@ -1,77 +0,0 @@
-/* err/error.c
- *
- * Copyright (C) 1996, 1997, 1998, 1999, 2000, 2007 Gerard Jungman, Brian Gough
- *
- * 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, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
- */
-
-#include <stddef.h>
-#include <stdlib.h>
-#include <stdio.h>
-
-#include "gsl_errno.h"
-#include "gsl_message.h"
-
-gsl_error_handler_t * gsl_error_handler = NULL;
-
-static void no_error_handler (const char *reason, const char *file, int line, int gsl_errno);
-
-void
-gsl_error (const char * reason, const char * file, int line, int gsl_errno)
-{
- if (gsl_error_handler)
- {
- (*gsl_error_handler) (reason, file, line, gsl_errno);
- return ;
- }
-
- gsl_stream_printf ("ERROR", file, line, reason);
-
- fflush (stdout);
- fprintf (stderr, "Default GSL error handler invoked.\n");
- fflush (stderr);
-
- abort ();
-}
-
-gsl_error_handler_t *
-gsl_set_error_handler (gsl_error_handler_t * new_handler)
-{
- gsl_error_handler_t * previous_handler = gsl_error_handler;
- gsl_error_handler = new_handler;
- return previous_handler;
-}
-
-
-gsl_error_handler_t *
-gsl_set_error_handler_off (void)
-{
- gsl_error_handler_t * previous_handler = gsl_error_handler;
- gsl_error_handler = no_error_handler;
- return previous_handler;
-}
-
-static void
-no_error_handler (const char *reason, const char *file, int line, int gsl_errno)
-{
- /* do nothing */
- (void) reason;
- (void) file;
- (void) line;
- (void) gsl_errno;
- return;
-}
-
-
diff --git a/src/gsl/gsl_combination.h b/src/gsl/gsl_combination.h
deleted file mode 100644
index ee13dfb..0000000
--- a/src/gsl/gsl_combination.h
+++ /dev/null
@@ -1,76 +0,0 @@
-/* combination/gsl_combination.h
- * based on permutation/gsl_permutation.h by Brian Gough
- *
- * Copyright (C) 2001 Szymon Jaroszewicz
- *
- * 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, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
- */
-
-#ifndef __GSL_COMBINATION_H__
-#define __GSL_COMBINATION_H__
-
-#include <stdlib.h>
-#include "gsl_errno.h"
-
-#undef __BEGIN_DECLS
-#undef __END_DECLS
-#ifdef __cplusplus
-# define __BEGIN_DECLS extern "C" {
-# define __END_DECLS }
-#else
-# define __BEGIN_DECLS /* empty */
-# define __END_DECLS /* empty */
-#endif
-
-__BEGIN_DECLS
-
-struct gsl_combination_struct
-{
- size_t n;
- size_t k;
- size_t *data;
-};
-
-typedef struct gsl_combination_struct gsl_combination;
-
-gsl_combination *gsl_combination_alloc (const size_t n, const size_t k);
-gsl_combination *gsl_combination_calloc (const size_t n, const size_t k);
-void gsl_combination_init_first (gsl_combination * c);
-void gsl_combination_init_last (gsl_combination * c);
-void gsl_combination_free (gsl_combination * c);
-int gsl_combination_memcpy (gsl_combination * dest, const gsl_combination * src);
-
-int gsl_combination_fread (FILE * stream, gsl_combination * c);
-int gsl_combination_fwrite (FILE * stream, const gsl_combination * c);
-int gsl_combination_fscanf (FILE * stream, gsl_combination * c);
-int gsl_combination_fprintf (FILE * stream, const gsl_combination * c, const char *format);
-
-size_t gsl_combination_n (const gsl_combination * c);
-size_t gsl_combination_k (const gsl_combination * c);
-size_t * gsl_combination_data (const gsl_combination * c);
-
-int gsl_combination_valid (gsl_combination * c);
-int gsl_combination_next (gsl_combination * c);
-int gsl_combination_prev (gsl_combination * c);
-
-static inline size_t
-gsl_combination_get (const gsl_combination * c, const size_t i)
-{
- return c->data[i];
-}
-
-__END_DECLS
-
-#endif /* __GSL_COMBINATION_H__ */
diff --git a/src/gsl/gsl_errno.h b/src/gsl/gsl_errno.h
deleted file mode 100644
index 76a998c..0000000
--- a/src/gsl/gsl_errno.h
+++ /dev/null
@@ -1,153 +0,0 @@
-/* err/gsl_errno.h
- *
- * Copyright (C) 1996, 1997, 1998, 1999, 2000, 2007 Gerard Jungman, Brian Gough
- *
- * 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, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
- */
-
-#ifndef __GSL_ERRNO_H__
-#define __GSL_ERRNO_H__
-
-#include <stdio.h>
-#include <errno.h>
-
-#undef __BEGIN_DECLS
-#undef __END_DECLS
-#ifdef __cplusplus
-# define __BEGIN_DECLS extern "C" {
-# define __END_DECLS }
-#else
-# define __BEGIN_DECLS /* empty */
-# define __END_DECLS /* empty */
-#endif
-
-__BEGIN_DECLS
-
-enum {
- GSL_SUCCESS = 0,
- GSL_FAILURE = -1,
- GSL_CONTINUE = -2, /* iteration has not converged */
- GSL_EDOM = 1, /* input domain error, e.g sqrt(-1) */
- GSL_ERANGE = 2, /* output range error, e.g. exp(1e100) */
- GSL_EFAULT = 3, /* invalid pointer */
- GSL_EINVAL = 4, /* invalid argument supplied by user */
- GSL_EFAILED = 5, /* generic failure */
- GSL_EFACTOR = 6, /* factorization failed */
- GSL_ESANITY = 7, /* sanity check failed - shouldn't happen */
- GSL_ENOMEM = 8, /* malloc failed */
- GSL_EBADFUNC = 9, /* problem with user-supplied function */
- GSL_ERUNAWAY = 10, /* iterative process is out of control */
- GSL_EMAXITER = 11, /* exceeded max number of iterations */
- GSL_EZERODIV = 12, /* tried to divide by zero */
- GSL_EBADTOL = 13, /* user specified an invalid tolerance */
- GSL_ETOL = 14, /* failed to reach the specified tolerance */
- GSL_EUNDRFLW = 15, /* underflow */
- GSL_EOVRFLW = 16, /* overflow */
- GSL_ELOSS = 17, /* loss of accuracy */
- GSL_EROUND = 18, /* failed because of roundoff error */
- GSL_EBADLEN = 19, /* matrix, vector lengths are not conformant */
- GSL_ENOTSQR = 20, /* matrix not square */
- GSL_ESING = 21, /* apparent singularity detected */
- GSL_EDIVERGE = 22, /* integral or series is divergent */
- GSL_EUNSUP = 23, /* requested feature is not supported by the hardware */
- GSL_EUNIMPL = 24, /* requested feature not (yet) implemented */
- GSL_ECACHE = 25, /* cache limit exceeded */
- GSL_ETABLE = 26, /* table limit exceeded */
- GSL_ENOPROG = 27, /* iteration is not making progress towards solution */
- GSL_ENOPROGJ = 28, /* jacobian evaluations are not improving the solution */
- GSL_ETOLF = 29, /* cannot reach the specified tolerance in F */
- GSL_ETOLX = 30, /* cannot reach the specified tolerance in X */
- GSL_ETOLG = 31, /* cannot reach the specified tolerance in gradient */
- GSL_EOF = 32 /* end of file */
-} ;
-
-void gsl_error (const char * reason, const char * file, int line,
- int gsl_errno);
-
-void gsl_stream_printf (const char *label, const char *file,
- int line, const char *reason);
-
-const char * gsl_strerror (const int gsl_errno);
-
-typedef void gsl_error_handler_t (const char * reason, const char * file,
- int line, int gsl_errno);
-
-typedef void gsl_stream_handler_t (const char * label, const char * file,
- int line, const char * reason);
-
-gsl_error_handler_t *
-gsl_set_error_handler (gsl_error_handler_t * new_handler);
-
-gsl_error_handler_t *
-gsl_set_error_handler_off (void);
-
-gsl_stream_handler_t *
-gsl_set_stream_handler (gsl_stream_handler_t * new_handler);
-
-FILE * gsl_set_stream (FILE * new_stream);
-
-/* GSL_ERROR: call the error handler, and return the error code */
-
-#define GSL_ERROR(reason, gsl_errno) \
- do { \
- gsl_error (reason, __FILE__, __LINE__, gsl_errno) ; \
- return gsl_errno ; \
- } while (0)
-
-/* GSL_ERROR_VAL: call the error handler, and return the given value */
-
-#define GSL_ERROR_VAL(reason, gsl_errno, value) \
- do { \
- gsl_error (reason, __FILE__, __LINE__, gsl_errno) ; \
- return value ; \
- } while (0)
-
-/* GSL_ERROR_VOID: call the error handler, and then return
- (for void functions which still need to generate an error) */
-
-#define GSL_ERROR_VOID(reason, gsl_errno) \
- do { \
- gsl_error (reason, __FILE__, __LINE__, gsl_errno) ; \
- return ; \
- } while (0)
-
-/* GSL_ERROR_NULL suitable for out-of-memory conditions */
-
-#define GSL_ERROR_NULL(reason, gsl_errno) GSL_ERROR_VAL(reason, gsl_errno, 0)
-
-/* Sometimes you have several status results returned from
- * function calls and you want to combine them in some sensible
- * way. You cannot produce a "total" status condition, but you can
- * pick one from a set of conditions based on an implied hierarchy.
- *
- * In other words:
- * you have: status_a, status_b, ...
- * you want: status = (status_a if it is bad, or status_b if it is bad,...)
- *
- * In this example you consider status_a to be more important and
- * it is checked first, followed by the others in the order specified.
- *
- * Here are some dumb macros to do this.
- */
-#define GSL_ERROR_SELECT_2(a,b) ((a) != GSL_SUCCESS ? (a) : ((b) != GSL_SUCCESS ? (b) : GSL_SUCCESS))
-#define GSL_ERROR_SELECT_3(a,b,c) ((a) != GSL_SUCCESS ? (a) : GSL_ERROR_SELECT_2(b,c))
-#define GSL_ERROR_SELECT_4(a,b,c,d) ((a) != GSL_SUCCESS ? (a) : GSL_ERROR_SELECT_3(b,c,d))
-#define GSL_ERROR_SELECT_5(a,b,c,d,e) ((a) != GSL_SUCCESS ? (a) : GSL_ERROR_SELECT_4(b,c,d,e))
-
-#define GSL_STATUS_UPDATE(sp, s) do { if ((s) != GSL_SUCCESS) *(sp) = (s);} while(0)
-
-__END_DECLS
-
-#endif /* __GSL_ERRNO_H__ */
diff --git a/src/gsl/gsl_message.h b/src/gsl/gsl_message.h
deleted file mode 100644
index 2061ddb..0000000
--- a/src/gsl/gsl_message.h
+++ /dev/null
@@ -1,79 +0,0 @@
-/* err/gsl_message.h
- *
- * Copyright (C) 1996, 1997, 1998, 1999, 2000, 2007 Gerard Jungman, Brian Gough
- *
- * 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, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
- */
-
-#ifndef __GSL_MESSAGE_H__
-#define __GSL_MESSAGE_H__
-
-#undef __BEGIN_DECLS
-#undef __END_DECLS
-#ifdef __cplusplus
-# define __BEGIN_DECLS extern "C" {
-# define __END_DECLS }
-#else
-# define __BEGIN_DECLS /* empty */
-# define __END_DECLS /* empty */
-#endif
-
-__BEGIN_DECLS
-
-/* Provide a general messaging service for client use. Messages can
- * be selectively turned off at compile time by defining an
- * appropriate message mask. Client code which uses the GSL_MESSAGE()
- * macro must provide a mask which is or'ed with the GSL_MESSAGE_MASK.
- *
- * The messaging service can be completely turned off
- * by defining GSL_MESSAGING_OFF. */
-
-void gsl_message(const char * message, const char * file, int line,
- unsigned int mask);
-
-#ifndef GSL_MESSAGE_MASK
-#define GSL_MESSAGE_MASK 0xffffffffu /* default all messages allowed */
-#endif
-
-unsigned int gsl_message_mask ;
-
-/* Provide some symolic masks for client ease of use. */
-
-enum {
- GSL_MESSAGE_MASK_A = 1,
- GSL_MESSAGE_MASK_B = 2,
- GSL_MESSAGE_MASK_C = 4,
- GSL_MESSAGE_MASK_D = 8,
- GSL_MESSAGE_MASK_E = 16,
- GSL_MESSAGE_MASK_F = 32,
- GSL_MESSAGE_MASK_G = 64,
- GSL_MESSAGE_MASK_H = 128
-} ;
-
-#ifdef GSL_MESSAGING_OFF /* throw away messages */
-#define GSL_MESSAGE(message, mask) do { } while(0)
-#else /* output all messages */
-#define GSL_MESSAGE(message, mask) \
- do { \
- if (mask & GSL_MESSAGE_MASK) \
- gsl_message (message, __FILE__, __LINE__, mask) ; \
- } while (0)
-#endif
-
-__END_DECLS
-
-#endif /* __GSL_MESSAGE_H__ */
-
-
diff --git a/src/gsl/init.c b/src/gsl/init.c
deleted file mode 100644
index 3a50c78..0000000
--- a/src/gsl/init.c
+++ /dev/null
@@ -1,127 +0,0 @@
-/* combination/init.c
- * based on permutation/init.c by Brian Gough
- *
- * Copyright (C) 2001 Szymon Jaroszewicz
- * Copyright (C) 2009 Brian Gough
- *
- * 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, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
- */
-
-#include <stdlib.h>
-#include "gsl_errno.h"
-#include "gsl_combination.h"
-
-gsl_combination *
-gsl_combination_alloc (const size_t n, const size_t k)
-{
- gsl_combination * c;
-
- if (n == 0)
- {
- GSL_ERROR_VAL ("combination parameter n must be positive integer",
- GSL_EDOM, 0);
- }
- if (k > n)
- {
- GSL_ERROR_VAL ("combination length k must be an integer less than or equal to n",
- GSL_EDOM, 0);
- }
- c = (gsl_combination *) malloc (sizeof (gsl_combination));
-
- if (c == 0)
- {
- GSL_ERROR_VAL ("failed to allocate space for combination struct",
- GSL_ENOMEM, 0);
- }
-
- if (k > 0)
- {
- c->data = (size_t *) malloc (k * sizeof (size_t));
-
- if (c->data == 0)
- {
- free (c); /* exception in constructor, avoid memory leak */
-
- GSL_ERROR_VAL ("failed to allocate space for combination data",
- GSL_ENOMEM, 0);
- }
- }
- else
- {
- c->data = 0;
- }
-
- c->n = n;
- c->k = k;
-
- return c;
-}
-
-gsl_combination *
-gsl_combination_calloc (const size_t n, const size_t k)
-{
- size_t i;
-
- gsl_combination * c = gsl_combination_alloc (n, k);
-
- if (c == 0)
- return 0;
-
- /* initialize combination to identity */
-
- for (i = 0; i < k; i++)
- {
- c->data[i] = i;
- }
-
- return c;
-}
-
-void
-gsl_combination_init_first (gsl_combination * c)
-{
- const size_t k = c->k ;
- size_t i;
-
- /* initialize combination to identity */
-
- for (i = 0; i < k; i++)
- {
- c->data[i] = i;
- }
-}
-
-void
-gsl_combination_init_last (gsl_combination * c)
-{
- const size_t k = c->k ;
- size_t i;
- size_t n = c->n;
-
- /* initialize combination to identity */
-
- for (i = 0; i < k; i++)
- {
- c->data[i] = n - k + i;
- }
-}
-
-void
-gsl_combination_free (gsl_combination * c)
-{
- if (c == NULL) return;
- if (c->k > 0) free (c->data);
- free (c);
-}
diff --git a/src/gsl/message.c b/src/gsl/message.c
deleted file mode 100644
index a8961b0..0000000
--- a/src/gsl/message.c
+++ /dev/null
@@ -1,37 +0,0 @@
-/* err/message.c
- *
- * Copyright (C) 1996, 1997, 1998, 1999, 2000, 2007 Gerard Jungman, Brian Gough
- *
- * 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, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
- */
-
-#include <stddef.h>
-#include <stdlib.h>
-#include <stdio.h>
-
-#include "gsl_errno.h"
-#include "gsl_message.h"
-
-unsigned int gsl_message_mask = GSL_MESSAGE_MASK;
-
-void
-gsl_message (const char * reason, const char * file, int line,
- unsigned int mask)
-{
- if (mask & gsl_message_mask)
- {
- gsl_stream_printf ("MESSAGE", file, line, reason);
- }
-}
diff --git a/src/gsl/stream.c b/src/gsl/stream.c
deleted file mode 100644
index 8cf2ef1..0000000
--- a/src/gsl/stream.c
+++ /dev/null
@@ -1,65 +0,0 @@
-/* err/stream.c
- *
- * Copyright (C) 1996, 1997, 1998, 1999, 2000, 2007 Gerard Jungman, Brian Gough
- *
- * 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, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
- */
-
-#include <stddef.h>
-#include <stdlib.h>
-#include <stdio.h>
-
-#include "gsl_errno.h"
-#include "gsl_message.h"
-
-FILE * gsl_stream = NULL ;
-gsl_stream_handler_t * gsl_stream_handler = NULL;
-
-void
-gsl_stream_printf (const char *label, const char *file, int line,
- const char *reason)
-{
- if (gsl_stream == NULL)
- {
- gsl_stream = stderr;
- }
- if (gsl_stream_handler)
- {
- (*gsl_stream_handler) (label, file, line, reason);
- return;
- }
- fprintf (gsl_stream, "gsl: %s:%d: %s: %s\n", file, line, label, reason);
-
-}
-
-gsl_stream_handler_t *
-gsl_set_stream_handler (gsl_stream_handler_t * new_handler)
-{
- gsl_stream_handler_t * previous_handler = gsl_stream_handler;
- gsl_stream_handler = new_handler;
- return previous_handler;
-}
-
-FILE *
-gsl_set_stream (FILE * new_stream)
-{
- FILE * previous_stream;
- if (gsl_stream == NULL) {
- gsl_stream = stderr;
- }
- previous_stream = gsl_stream;
- gsl_stream = new_stream;
- return previous_stream;
-}
diff --git a/src/gsl/strerror.c b/src/gsl/strerror.c
deleted file mode 100644
index 398a132..0000000
--- a/src/gsl/strerror.c
+++ /dev/null
@@ -1,100 +0,0 @@
-/* err/strerror.c
- *
- * Copyright (C) 1996, 1997, 1998, 1999, 2000, 2007 Gerard Jungman, Brian Gough
- *
- * 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, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
- */
-
-#include "gsl_errno.h"
-
-const char *
-gsl_strerror (const int gsl_errno)
-{
- switch (gsl_errno)
- {
- case GSL_SUCCESS:
- return "success" ;
- case GSL_FAILURE:
- return "failure" ;
- case GSL_CONTINUE:
- return "the iteration has not converged yet";
- case GSL_EDOM:
- return "input domain error" ;
- case GSL_ERANGE:
- return "output range error" ;
- case GSL_EFAULT:
- return "invalid pointer" ;
- case GSL_EINVAL:
- return "invalid argument supplied by user" ;
- case GSL_EFAILED:
- return "generic failure" ;
- case GSL_EFACTOR:
- return "factorization failed" ;
- case GSL_ESANITY:
- return "sanity check failed - shouldn't happen" ;
- case GSL_ENOMEM:
- return "malloc failed" ;
- case GSL_EBADFUNC:
- return "problem with user-supplied function";
- case GSL_ERUNAWAY:
- return "iterative process is out of control";
- case GSL_EMAXITER:
- return "exceeded max number of iterations" ;
- case GSL_EZERODIV:
- return "tried to divide by zero" ;
- case GSL_EBADTOL:
- return "specified tolerance is invalid or theoretically unattainable" ;
- case GSL_ETOL:
- return "failed to reach the specified tolerance" ;
- case GSL_EUNDRFLW:
- return "underflow" ;
- case GSL_EOVRFLW:
- return "overflow" ;
- case GSL_ELOSS:
- return "loss of accuracy" ;
- case GSL_EROUND:
- return "roundoff error" ;
- case GSL_EBADLEN:
- return "matrix/vector sizes are not conformant" ;
- case GSL_ENOTSQR:
- return "matrix not square" ;
- case GSL_ESING:
- return "singularity or extremely bad function behavior detected" ;
- case GSL_EDIVERGE:
- return "integral or series is divergent" ;
- case GSL_EUNSUP:
- return "the required feature is not supported by this hardware platform";
- case GSL_EUNIMPL:
- return "the requested feature is not (yet) implemented";
- case GSL_ECACHE:
- return "cache limit exceeded";
- case GSL_ETABLE:
- return "table limit exceeded";
- case GSL_ENOPROG:
- return "iteration is not making progress towards solution";
- case GSL_ENOPROGJ:
- return "jacobian evaluations are not improving the solution";
- case GSL_ETOLF:
- return "cannot reach the specified tolerance in F";
- case GSL_ETOLX:
- return "cannot reach the specified tolerance in X";
- case GSL_ETOLG:
- return "cannot reach the specified tolerance in gradient";
- case GSL_EOF:
- return "end of file";
- default:
- return "unknown error code" ;
- }
-}
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/.travis.yml b/src/libqes/.travis.yml
deleted file mode 100644
index aa41a19..0000000
--- a/src/libqes/.travis.yml
+++ /dev/null
@@ -1,38 +0,0 @@
-language: c
-
-env:
- - BUILD_TYPE=Release
- - BUILD_TYPE=Debug
- - BUILD_TYPE=Coverage
-
-compiler:
- - clang
- - gcc
-
-install:
- - sudo apt-get install lcov python-pip
- - mkdir zlib && cd zlib
- - wget http://zlib.net/zlib-1.2.8.tar.gz
- - tar xvxf zlib-1.2.8.tar.gz
- - cd zlib-1.2.8
- - ./configure
- - make
- - sudo make install
- - cd ../..
- - sudo pip install cpp-coveralls
- - git submodule update --init
- - 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
- - if [ $static == "TRUE" ] ; then test -f ../target/lib/libqes.a; else test -f ../target/lib/libqes.so ; fi
-
-after_success:
- - cd ..
- - if [ "$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 bb91d87..0000000
--- a/src/libqes/CMakeLists.txt
+++ /dev/null
@@ -1,154 +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)
-
-###############################
-## 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 ${NO_ZLIB})
- FIND_PACKAGE(ZLIB 1.2.1 REQUIRED)
- CHECK_LIBRARY_EXISTS(${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}
- ${OpenMP_C_FLAGS})
-
-##########################
-## Set Compiler Options ##
-##########################
-
-# Set GCC-specific options
-IF (CMAKE_COMPILER_IS_GNUCC)
- SET(WEXTRA_FLAGS "${WEXTRA_FLAGS} -Woverride-init -Wnormalized=id -Wlogical-op")
- EXECUTE_PROCESS(COMMAND ${CMAKE_C_COMPILER} -dumpversion OUTPUT_VARIABLE GCC_VERSION)
- IF (${GCC_VERSION} VERSION_GREATER 4.9 OR ${GCC_VERSION} VERSION_EQUAL 4.9)
- SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fdiagnostics-color=always")
- ENDIF()
-ENDIF()
-
-# Set CFLAGS
-SET(WEXTRA_FLAGS "${WEXTRA_FLAGS} -Wstack-protector -Wfloat-equal")
-SET(WEXTRA_FLAGS "${WEXTRA_FLAGS} -Wundef -Wpointer-arith -Wstrict-prototypes")
-SET(WEXTRA_FLAGS "${WEXTRA_FLAGS} -Wmissing-prototypes -Wwrite-strings -Wredundant-decls")
-SET(WEXTRA_FLAGS "${WEXTRA_FLAGS} -Wchar-subscripts -Wcomment -Wformat=2 -Wwrite-strings")
-SET(WEXTRA_FLAGS "${WEXTRA_FLAGS} -Wmissing-declarations -Wredundant-decls -Wnested-externs")
-SET(WEXTRA_FLAGS "${WEXTRA_FLAGS} -Wbad-function-cast -Wswitch-enum -Winit-self")
-SET(WEXTRA_FLAGS "${WEXTRA_FLAGS} -Wmissing-field-initializers -Wdeclaration-after-statement")
-SET(WEXTRA_FLAGS "${WEXTRA_FLAGS} -Wold-style-definition -Waddress -Wmissing-noreturn ")
-SET(WEXTRA_FLAGS "${WEXTRA_FLAGS} -Wstrict-overflow=1 -Wextra -Warray-bounds -Wall")
-
-SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${LIBQES_DEPENDS_CFLAGS} -std=gnu99 ${WEXTRA_FLAGS}")
-
-SET(CMAKE_C_FLAGS_DEBUG "-ggdb")
-SET(CMAKE_C_FLAGS_RELEASE "-O3")
-
-# 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)
-ADD_SUBDIRECTORY(test)
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
-free programs, and that you know you can do these things.
-
- To protect your rights, we need to prevent others from denying you
-these rights or asking you to surrender the rights. Therefore, you have
-certain responsibilities if you distribute copies of the software, or if
-you modify it: responsibilities to respect the freedom of others.
-
- For example, if you distribute copies of such a program, whether
-gratis or for a fee, you must pass on to the recipients the same
-freedoms that you received. You must make sure that they, too, receive
-or can get the source code. And you must show them these terms so they
-know their rights.
-
- Developers that use the GNU GPL protect your rights with two steps:
-(1) assert copyright on the software, and (2) offer you this License
-giving you legal permission to copy, distribute and/or modify it.
-
- For the developers' and authors' protection, the GPL clearly explains
-that there is no warranty for this free software. For both users' and
-authors' sake, the GPL requires that modified versions be marked as
-changed, so that their problems will not be attributed erroneously to
-authors of previous versions.
-
- Some devices are designed to deny users access to install or run
-modified versions of the software inside them, although the manufacturer
-can do so. This is fundamentally incompatible with the aim of
-protecting users' freedom to change the software. The systematic
-pattern of such abuse occurs in the area of products for individuals to
-use, which is precisely where it is most unacceptable. Therefore, we
-have designed this version of the GPL to prohibit the practice for those
-products. If such problems arise substantially in other domains, we
-stand ready to extend this provision to those domains in future versions
-of the GPL, as needed to protect the freedom of users.
-
- Finally, every program is threatened constantly by software patents.
-States should not allow patents to restrict development and use of
-software on general-purpose computers, but in those that do, we wish to
-avoid the special danger that patents applied to a free program could
-make it effectively proprietary. To prevent this, the GPL assures that
-patents cannot be used to render the program non-free.
-
- The precise terms and conditions for copying, distribution and
-modification follow.
-
- TERMS AND CONDITIONS
-
- 0. Definitions.
-
- "This License" refers to version 3 of the GNU General Public License.
-
- "Copyright" also means copyright-like laws that apply to other kinds of
-works, such as semiconductor masks.
-
- "The Program" refers to any copyrightable work licensed under this
-License. Each licensee is addressed as "you". "Licensees" and
-"recipients" may be individuals or organizations.
-
- To "modify" a work means to copy from or adapt all or part of the work
-in a fashion requiring copyright permission, other than the making of an
-exact copy. The resulting work is called a "modified version" of the
-earlier work or a work "based on" the earlier work.
-
- A "covered work" means either the unmodified Program or a work based
-on the Program.
-
- To "propagate" a work means to do anything with it that, without
-permission, would make you directly or secondarily liable for
-infringement under applicable copyright law, except executing it on a
-computer or modifying a private copy. Propagation includes copying,
-distribution (with or without modification), making available to the
-public, and in some countries other activities as well.
-
- To "convey" a work means any kind of propagation that enables other
-parties to make or receive copies. Mere interaction with a user through
-a computer network, with no transfer of a copy, is not conveying.
-
- An interactive user interface displays "Appropriate Legal Notices"
-to the extent that it includes a convenient and prominently visible
-feature that (1) displays an appropriate copyright notice, and (2)
-tells the user that there is no warranty for the work (except to the
-extent that warranties are provided), that licensees may convey the
-work under this License, and how to view a copy of this License. If
-the interface presents a list of user commands or options, such as a
-menu, a prominent item in the list meets this criterion.
-
- 1. Source Code.
-
- The "source code" for a work means the preferred form of the work
-for making modifications to it. "Object code" means any non-source
-form of a work.
-
- A "Standard Interface" means an interface that either is an official
-standard defined by a recognized standards body, or, in the case of
-interfaces specified for a particular programming language, one that
-is widely used among developers working in that language.
-
- The "System Libraries" of an executable work include anything, other
-than the work as a whole, that (a) is included in the normal form of
-packaging a Major Component, but which is not part of that Major
-Component, and (b) serves only to enable use of the work with that
-Major Component, or to implement a Standard Interface for which an
-implementation is available to the public in source code form. A
-"Major Component", in this context, means a major essential component
-(kernel, window system, and so on) of the specific operating system
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-public statement of acceptance of a version permanently authorizes you
-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
-later version.
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-an absolute waiver of all civil liability in connection with the
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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/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 295217c..0000000
--- a/src/libqes/cmake-modules/FindLIBQES.cmake
+++ /dev/null
@@ -1,83 +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
-#
-# Distributed under the OSI-approved BSD License (the "License");
-# see accompanying file Copyright.txt for details.
-#
-# This software is distributed WITHOUT ANY WARRANTY; without even the
-# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the License for more information.
-#=============================================================================
-# (To distribute this file outside of CMake, substitute the full
-# License text for the above reference.)
-
-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 "${HEAD_HASH}" HEAD_HASH)
-endif()
diff --git a/src/libqes/cmake-modules/GitSemVer.cmake b/src/libqes/cmake-modules/GitSemVer.cmake
deleted file mode 100644
index 290b8dd..0000000
--- a/src/libqes/cmake-modules/GitSemVer.cmake
+++ /dev/null
@@ -1,27 +0,0 @@
-INCLUDE(GetGitRevisionDescription)
-
-function(GetGitSemVer _var)
- get_git_head_revision(rev hash)
- git_get_exact_tag(tag)
-
- IF(NOT "${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 9e4e458..0000000
--- a/src/libqes/src/CMakeLists.txt
+++ /dev/null
@@ -1,16 +0,0 @@
-file(GLOB LIBQES_SOURCES qes_*.c)
-
-# Targets
-ADD_LIBRARY(qes_static STATIC ${LIBQES_SOURCES})
-SET_TARGET_PROPERTIES(qes_static PROPERTIES OUTPUT_NAME qes)
-TARGET_LINK_LIBRARIES(qes_static ${LIBQES_DEPENDS_LIBS})
-ADD_LIBRARY(qes SHARED ${LIBQES_SOURCES})
-TARGET_LINK_LIBRARIES(qes ${LIBQES_DEPENDS_LIBS})
-
-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 89138f3..0000000
--- a/src/libqes/src/qes.h
+++ /dev/null
@@ -1,26 +0,0 @@
-/*
- * ==========================================================================
- *
- * 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 7c5e1b2..0000000
--- a/src/libqes/src/qes_compat.c
+++ /dev/null
@@ -1,66 +0,0 @@
-/*
- * ============================================================================
- *
- * 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 33fc07b..0000000
--- a/src/libqes/src/qes_compat.h
+++ /dev/null
@@ -1,29 +0,0 @@
-/*
- * ============================================================================
- *
- * 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 a8dc840..0000000
--- a/src/libqes/src/qes_config.h.in
+++ /dev/null
@@ -1,76 +0,0 @@
-/*
- * ============================================================================
- *
- * 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 25bcaad..0000000
--- a/src/libqes/src/qes_file.c
+++ /dev/null
@@ -1,496 +0,0 @@
-/*
- * ============================================================================
- *
- * 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 */
- 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
-Paramters: 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 6e8f458..0000000
--- a/src/libqes/src/qes_file.h
+++ /dev/null
@@ -1,213 +0,0 @@
-/*
- * ============================================================================
- *
- * 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
-Paramters: 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
-Paramters: 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
-Paramters: 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
-Paramters: 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
-Paramters: 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 4ac1497..0000000
--- a/src/libqes/src/qes_libgnu.c
+++ /dev/null
@@ -1,16 +0,0 @@
-/*
- * ============================================================================
- *
- * 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 3993a42..0000000
--- a/src/libqes/src/qes_libgnu.h
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * ============================================================================
- *
- * 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 seperate 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 6c19a1d..0000000
--- a/src/libqes/src/qes_log.c
+++ /dev/null
@@ -1,251 +0,0 @@
-/*
- * ============================================================================
- *
- * 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 614e0ad..0000000
--- a/src/libqes/src/qes_log.h
+++ /dev/null
@@ -1,150 +0,0 @@
-/*
- * ============================================================================
- *
- * 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 inbetween 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) ({ _qes_logger_destroy(l); l = NULL; })
-
-
-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) ({ _qes_log_entry_destroy(l); l = NULL; })
-
-
-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 1599b1a..0000000
--- a/src/libqes/src/qes_match.c
+++ /dev/null
@@ -1,83 +0,0 @@
-/*
- * ============================================================================
- *
- * 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 analagous 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 lenght 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 31135a4..0000000
--- a/src/libqes/src/qes_match.h
+++ /dev/null
@@ -1,50 +0,0 @@
-/*
- * ============================================================================
- *
- * 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
-Paramters: 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
-Paramters: 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 9384fa8..0000000
--- a/src/libqes/src/qes_seq.c
+++ /dev/null
@@ -1,157 +0,0 @@
-/*
- * ============================================================================
- *
- * Filename: qes_seq.c
- *
- * Description: Sequence structures
- * License: GPLv3+
- * Author: Kevin Murray, spam at kdmurray.id.au
- *
- * ============================================================================
- */
-
-#include "qes_seq.h"
-
-
-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;
- }
- 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 (qes_seq_fill_qual(seqobj, qual, strlen(qual)) != 0) return 1;
- return 0;
-}
-
-/*=== FUNCTION ============================================================*
-Name: qes_seq_destroy
-Paramters: 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);
- }
-}
diff --git a/src/libqes/src/qes_seq.h b/src/libqes/src/qes_seq.h
deleted file mode 100644
index fb2c65a..0000000
--- a/src/libqes/src/qes_seq.h
+++ /dev/null
@@ -1,187 +0,0 @@
-/*
- * ============================================================================
- *
- * 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 <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
-Paramters: 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);
-
-
-/*=== FUNCTION ============================================================*
-Name: qes_seq_ok
-Paramters: 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;
-}
-
-/*=== FUNCTION ============================================================*
-Name: qes_seq_fill_header
-Paramters: 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
-Paramters: 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);
-
-#if 0
-/*=== FUNCTION ============================================================*
-Name: qes_seq_print
-Paramters: const struct qes_seq *: seq to print
- qes_seqfile_format_t: file format to print in.
- FILE *: open file stream to print to.
-Description: Print ``seq`` in formatted per ``format`` to ``stream``.
-Returns: int: 1 on success, 0 on failure.
- *===========================================================================*/
-extern int qes_seq_print (const struct qes_seq *seq,
- enum qes_seqfile_format fmt, FILE *stream);
-#endif
-
-/*=== FUNCTION ============================================================*
-Name: qes_seq_destroy
-Paramters: 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 b876252..0000000
--- a/src/libqes/src/qes_seqfile.c
+++ /dev/null
@@ -1,319 +0,0 @@
-/*
- * ============================================================================
- *
- * 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);
- /* 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(seqfile->qf, seq->seq.str + seq->seq.len,
- seq->seq.capacity - seq->seq.len - 1);
- if (len < 0) {
- goto error;
- }
- seq->seq.len += len - 1;
- seq->seq.str[seq->seq.len] = '\0';
- if (seq->seq.capacity - 1 <= seq->seq.len) {
- seq->seq.capacity = qes_roundupz(seq->seq.capacity);
- seq->seq.str = qes_realloc(seq->seq.str,
- sizeof(*seq->seq.str) * seq->seq.capacity);
- if (seq->seq.str == NULL) {
- goto error;
- }
- }
- }
- 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 eefccc6..0000000
--- a/src/libqes/src/qes_seqfile.h
+++ /dev/null
@@ -1,224 +0,0 @@
-/*
- * ============================================================================
- *
- * 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
-Paramters: 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
-Paramters: const struct qes_seqfile *file: File reference to check.
-Description: Check a file referenece ``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
-Paramters: 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 f8847d1..0000000
--- a/src/libqes/src/qes_sequtil.c
+++ /dev/null
@@ -1,256 +0,0 @@
-/*
- * ============================================================================
- *
- * 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 char
-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 11873f3..0000000
--- a/src/libqes/src/qes_sequtil.h
+++ /dev/null
@@ -1,23 +0,0 @@
-/*
- * ============================================================================
- *
- * 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 char 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 2bf83cf..0000000
--- a/src/libqes/src/qes_str.c
+++ /dev/null
@@ -1,36 +0,0 @@
-/*
- * ============================================================================
- *
- * 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)) {
- fprintf(stream, "%s", str->str);
- }
-}
-
-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 1066b90..0000000
--- a/src/libqes/src/qes_str.h
+++ /dev/null
@@ -1,135 +0,0 @@
-/*
- * ============================================================================
- *
- * 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_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);
- }
- 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));
- }
- /* FIXME: check for null after realloc */
- memcpy(str->str, cp, len);
- str->str[len] = '\0';
- str->len = len;
- return 1;
-}
-
-/*=== FUNCTION ============================================================*
-Name: qes_str_nullify
-Paramters: 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);
- memcpy(dest->str, src->str, src->capacity);
- return 0;
-}
-
-extern void qes_str_print (const struct qes_str *str, FILE *stream);
-
-/*=== FUNCTION ============================================================*
-Name: qes_str_destroy
-Paramters: 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
-Paramters: 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 bd14340..0000000
--- a/src/libqes/src/qes_util.c
+++ /dev/null
@@ -1,59 +0,0 @@
-/*
- * ============================================================================
- *
- * 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 961c581..0000000
--- a/src/libqes/src/qes_util.h
+++ /dev/null
@@ -1,236 +0,0 @@
-/*
- ============================================================================
- *
- * 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"
-#include "qes_compat.h"
-#include "qes_libgnu.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) ({
- #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 fdf2ed1..0000000
--- a/src/libqes/test/CMakeLists.txt
+++ /dev/null
@@ -1,36 +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})
-
-# 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 c088a61..0000000
--- a/src/libqes/test/benchmarks.c
+++ /dev/null
@@ -1,295 +0,0 @@
-/*
- * ============================================================================
- *
- * 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("Begining 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/log_test.txt b/src/libqes/test/data/log_test.txt
deleted file mode 100644
index 8254f87..0000000
--- a/src/libqes/test/data/log_test.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-Hello World
-Hello World
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/helpers.c b/src/libqes/test/helpers.c
deleted file mode 100644
index d98a733..0000000
--- a/src/libqes/test/helpers.c
+++ /dev/null
@@ -1,191 +0,0 @@
-/*
- * ============================================================================
- *
- * 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
-Paramters: 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
-Paramters: 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
-Paramters: 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
-Paramters: 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 111a060..0000000
--- a/src/libqes/test/helpers.h
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * ============================================================================
- *
- * 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/logdemo.c b/src/libqes/test/logdemo.c
deleted file mode 100644
index 82e13ae..0000000
--- a/src/libqes/test/logdemo.c
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * ============================================================================
- *
- * 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/test.c b/src/libqes/test/test.c
deleted file mode 100644
index 4252ef8..0000000
--- a/src/libqes/test/test.c
+++ /dev/null
@@ -1,64 +0,0 @@
-/*
- * ============================================================================
- *
- * 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 b2cfc24..0000000
--- a/src/libqes/test/test_file.c
+++ /dev/null
@@ -1,430 +0,0 @@
-/*
- * ============================================================================
- *
- * 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/existant.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 25d477d..0000000
--- a/src/libqes/test/test_helpers.c
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- * ============================================================================
- *
- * 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 726218d..0000000
--- a/src/libqes/test/test_log.c
+++ /dev/null
@@ -1,173 +0,0 @@
-/*
- * ============================================================================
- *
- * 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 acutal file as output */
- logger = qes_logger_create();
- tt_ptr_op(logger, !=, NULL);
- truth_fname = find_data_file("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 b287368..0000000
--- a/src/libqes/test/test_match.c
+++ /dev/null
@@ -1,89 +0,0 @@
-/*
- * ============================================================================
- *
- * 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 5b67b6a..0000000
--- a/src/libqes/test/test_seq.c
+++ /dev/null
@@ -1,422 +0,0 @@
-/*
- * ============================================================================
- *
- * 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_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},
- END_OF_TESTCASES
-};
diff --git a/src/libqes/test/test_seqfile.c b/src/libqes/test/test_seqfile.c
deleted file mode 100644
index 3639d82..0000000
--- a/src/libqes/test/test_seqfile.c
+++ /dev/null
@@ -1,402 +0,0 @@
-/*
- * ============================================================================
- *
- * 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.fasta");
- 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 bcf4a43..0000000
--- a/src/libqes/test/test_sequtil.c
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
- * ============================================================================
- *
- * 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 f4c6da7..0000000
--- a/src/libqes/test/test_util.c
+++ /dev/null
@@ -1,145 +0,0 @@
-/*
- * ============================================================================
- *
- * 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 4a66c85..0000000
--- a/src/libqes/test/testdata.c
+++ /dev/null
@@ -1,144 +0,0 @@
-/*
- * ============================================================================
- *
- * 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 48c374f..0000000
--- a/src/libqes/test/testdata.h
+++ /dev/null
@@ -1,49 +0,0 @@
-/*
- * ============================================================================
- *
- * 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 "}"
diff --git a/src/main.c b/src/main.c
index d396ab4..08aa30b 100644
--- a/src/main.c
+++ b/src/main.c
@@ -2,16 +2,22 @@
* ============================================================================
*
* Filename: axe_main.c
- *
* Description: Main loop for axe
+ * Copyright: 2014-2015 Kevin Murray <spam at kdmurray.id.au>
+ * License: GNU GPL v3+
+ *
+ * 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.
*
- * Version: 1.0
- * Created: 11/06/14 13:37:00
- * Revision: none
- * License: GPLv3+
- * Compiler: gcc, clang
+ * 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.
*
- * Author: Kevin Murray, spam at kdmurray.id.au
+ * You should have received a copy of the GNU General Public License along with
+ * this program. If not, see <http://www.gnu.org/licenses/>.
*
* ============================================================================
*/
@@ -24,7 +30,7 @@
static void
print_version(void)
{
- fprintf(stderr, "axe Version %s\n", AXE_VERSION);
+ fprintf(stderr, "AXE Version %s\n", AXE_VERSION);
}
static void
@@ -38,9 +44,9 @@ print_help(void)
fprintf(stderr, "must be. Likewise for a reverse/interleaved input. If either\n");
fprintf(stderr, "forward and/or reverse reads are given, interleaved input\n");
fprintf(stderr, "cannot be. However, one can input interleaved paired reads\n");
- fprintf(stderr, "and output seperate forwards and reverse reads, and vice versa.\n");
+ fprintf(stderr, "and output separate forwards and reverse reads, and vice versa.\n");
fprintf(stderr, "\n");
- fprintf(stderr, "The barcode file is a tab-seperated tabular file with an\n");
+ fprintf(stderr, "The barcode file is a tab-separated tabular file with an\n");
fprintf(stderr, "optional header, and has two alternative formats. The standard\n");
fprintf(stderr, "form (see below) is expected unless --combinatorial is given.\n");
fprintf(stderr, "\n");
@@ -63,9 +69,9 @@ print_usage(void)
{
print_version();
fprintf(stderr, "\nUSAGE:\n");
- fprintf(stderr, "axe [-mzc2pt] -b (-f [-r] | -i) (-F [-R] | -I)\n");
- fprintf(stderr, "axe -h\n");
- fprintf(stderr, "axe -v\n\n");
+ fprintf(stderr, "axe-demux [-mzc2pt] -b (-f [-r] | -i) (-F [-R] | -I)\n");
+ fprintf(stderr, "axe-demux -h\n");
+ fprintf(stderr, "axe-demux -v\n\n");
fprintf(stderr, "OPTIONS:\n");
fprintf(stderr, " -m, --mismatch\tMaximum hamming distance mismatch. [int, default 1]\n");
fprintf(stderr, " -z, --ziplevel\tGzip compression level, or 0 for plain text [int, default 0]\n");
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index 700ff01..e50a5fa 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -9,7 +9,7 @@ ADD_CUSTOM_TARGET(setup_tests ALL
${CMAKE_CURRENT_SOURCE_DIR}/data
${CMAKE_BINARY_DIR}/data
COMMAND ${CMAKE_COMMAND} -E copy
- ${CMAKE_CURRENT_SOURCE_DIR}/axe_integration.py
+ ${CMAKE_CURRENT_SOURCE_DIR}/axe_cli_tests.py
${CMAKE_BINARY_DIR}/bin
COMMAND ${CMAKE_COMMAND} -E make_directory
${CMAKE_BINARY_DIR}/out)
@@ -20,7 +20,7 @@ SET(COVERAGE_CMD test_axe)
SET(COVERAGE_OUT "${CMAKE_BINARY_DIR}/coverage_html")
ADD_TEST(NAME "IntegrationTests" COMMAND python
- ${CMAKE_BINARY_DIR}/bin/axe_integration.py
+ ${CMAKE_BINARY_DIR}/bin/axe_cli_tests.py
${CMAKE_BINARY_DIR})
IF (CMAKE_BUILD_TYPE STREQUAL "Coverage")
diff --git a/tests/axe_integration.py b/tests/axe_cli_tests.py
old mode 100644
new mode 100755
similarity index 92%
rename from tests/axe_integration.py
rename to tests/axe_cli_tests.py
index 8063175..7654c90
--- a/tests/axe_integration.py
+++ b/tests/axe_cli_tests.py
@@ -1,5 +1,6 @@
#!/usr/bin/env python
from __future__ import print_function
+import hashlib
import logging
import os
from os import path
@@ -11,23 +12,34 @@ import unittest
if len(sys.argv) < 2:
- print("USAGE: axe_integration.py $CMAKE_BINARY_DIR")
+ print("USAGE: axe_cli_tests.py $CMAKE_BINARY_DIR")
exit(-1)
CMAKE_BINARY_DIR = sys.argv.pop(1)
+def md5sum(filename):
+ h = hashlib.md5()
+ with open(filename, 'rb') as fh:
+ while True:
+ hunk = fh.read(1024 ** 2)
+ if not hunk:
+ break
+ h.update(hunk)
+ return h.hexdigest()
+
+
class AxeTest(unittest.TestCase):
maxDiff= None
def __init__(self, methodName='runTest'):
super(AxeTest, self).__init__(methodName)
self.data = path.join(CMAKE_BINARY_DIR, "data")
- self.out = path.join(CMAKE_BINARY_DIR, "out", "integration")
- self.axe = path.join(CMAKE_BINARY_DIR, "bin", "axe")
+ self.out = path.join(CMAKE_BINARY_DIR, "out", "cli_tests")
+ self.axe = path.join(CMAKE_BINARY_DIR, "bin", "axe-demux")
self.log = logging.getLogger("AxeTest")
if not path.exists(self.data) or not path.exists(self.axe):
- print("Please run axe_integration.py after compiling axe")
+ print("Please run axe_cli_tests.py after compiling axe")
exit(-1)
def setUp(self):
@@ -47,8 +59,7 @@ class AxeTest(unittest.TestCase):
dct = {}
for root, dirs, files in os.walk(self.out):
for fle in files:
- md5 = sp.check_output(["md5sum", path.join(root, fle)])
- md5, fle = md5.strip().split()
+ md5 = md5sum(path.join(root, fle))
dct[path.basename(fle)] = md5
return dct
--
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