Merge pull request #12 from whitwham/timeout

Add a time-out option

README.md

@@ -3,17 +3,20 @@ Stream files to and from iRODS.
 
 tears either reads from stdin and writes a file to iRODS or reads a file from iRODS and writes to stdout.  Basic usage for writing is:
 
-file_making_program | tears -w /path/to/irods/file
+`file_making_program | tears -w /path/to/irods/file`
 
 or for reading:
 
-tears /path/to/irods/file | file_receiving_program
+`tears /path/to/irods/file | file_receiving_program`
 
 Two things to note.  Firstly, tears will try to pick the best iRODS host to read or write from.  This can cause authentication problems and can be switched off by using the -d option.  Secondly, the iRODS file can be in the form of a URI (proposed [here](https://github.com/samtools/htslib/issues/229)).  The URI is of the form:
 
-irods://[irodsUserName%23irodsZone@][irodsHost][:irodsPort]/collection_path/data_object
-
+_irods://[irodsUserName%23irodsZone@][irodsHost][:irodsPort]/collection_path/data_object_
 
+### Build
 
+`autoreconf -i -f`
 
+`./configure --with-irods`
 
+`make`

configure.ac

@@ -1,6 +1,6 @@
 dnl                                             -*- Autoconf -*-
 AC_COPYRIGHT([
-Copyright (c) 2015-2016, 2018 Genome Research Ltd.
+Copyright (c) 2015-2016, 2018-2019 Genome Research Ltd.
 Author: Andrew Whitwham <[email protected]>
 
 This file is part of tears.
@@ -20,7 +20,7 @@ dnl Process this file with autoconf to produce a configure script.
 
 AC_PREREQ([2.68])
 
-AC_INIT([tears], [1.2.4], [[email protected]], [tears], [https://github.com/whitwham/tears])
+AC_INIT([tears], [1.3], [[email protected]], [tears], [https://github.com/whitwham/tears])
 AC_USE_SYSTEM_EXTENSIONS
 
 AM_INIT_AUTOMAKE([-Wall foreign])