Commit be7df110 authored by Alexandre Mestiashvili's avatar Alexandre Mestiashvili
Browse files

New upstream version 2.3.4.3

parent 157dbc20

CMakeLists.txt

+1 −1
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@@ -3,7 +3,7 @@ cmake_minimum_required(VERSION 2.8) 
cmake_policy(SET CMP0048 NEW)

cmake_policy(SET CMP0005 NEW)



project(bowtie2 LANGUAGES CXX VERSION "2.3.4.2")

project(bowtie2 LANGUAGES CXX VERSION "2.3.4.3")



enable_testing()

NEWS

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@@ -19,6 +19,14 @@ Please report any issues to the Bowtie 2 Github page or using the Sourceforge bu 
Version Release History

=======================



Version 2.3.4.3 - Sep 17, 2018



    * Fixed an issue causing `bowtie2-build` and `bowtie2-inspect`

      to output incomplete help text.

    * Fixed an issue causing `bowtie2-inspect` to crash.

    * Fixed an issue preventing `bowtie2` from processing paired and/or

      unpaired FASTQ reads together with interleaved FASTQ reads.



Version 2.3.4.2 - Aug 7, 2018



    * Fixed issue causing `bowtie2` to fail in `--fast-local` mode.

VERSION

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2.3.4.2
 
2.3.4.3

bowtie2-build

+8 −4
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@@ -29,15 +29,15 @@ import subprocess 
from collections import deque



def main():

    parser = argparse.ArgumentParser()

    parser = argparse.ArgumentParser(add_help = False)



    parser.add_argument('--large-index', action='store_true')

    parser.add_argument('--verbose', action='store_true')



    group = parser.add_mutually_exclusive_group()

    group.add_argument('--debug', action='store_true')

    group.add_argument('--sanitized', action='store_true')



    parser.add_argument('--verbose', action='store_true')

    parser.add_argument('--large-index', action='store_true')



    logging.basicConfig(level=logging.ERROR,

                        format='%(levelname)s: %(message)s'

                        )
@@ -51,8 +51,12 @@ def main(): 
    build_bin_spec      = os.path.join(ex_path,build_bin_s)



    script_options, argv = parser.parse_known_args()

    print_help = False

    argv = deque(argv)



    if '-h' in argv or '--help' in argv:

        print_help = True



    if script_options.verbose:

        logging.getLogger().setLevel(logging.INFO)

bowtie2-inspect

+2 −1
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@@ -22,6 +22,7 @@ 


import os

import imp

import sys

import inspect

import logging

import argparse
@@ -29,7 +30,7 @@ import subprocess 
from collections import deque



def main():

    parser = argparse.ArgumentParser()

    parser = argparse.ArgumentParser(add_help = False)



    group = parser.add_mutually_exclusive_group()

    group.add_argument('--debug', action='store_true')