README clarifications.

diff --git a/README b/README
deleted file mode 100644 (file)
index ad14efe..0000000
--- a/README
+++ /dev/null
@@ -1,69 +0,0 @@
-
-fastq-tools
-===========
-
-This package provides a number of small and efficient programs to perform common
-tasks with high throughput sequencing data in the FASTQ format. All of the
-programs work with typical FASTQ files as well as gzipped FASTQ files.
-
-
-index
------
-
-The following programs are provided. See the individual man pages for more
-information.
-
-
-*fastq-grep* : match sequences against regular expressions
-
-*fastq-kmers* : count k-mer occurrences
-
-*fastq-match* : (smith-waterman) local sequence alignment
-
-*fastq-uniq* : count duplicate reads
-
-
-install
--------
-
-On most systems, this is a simple `./configure && make install`.
-
-The only external dependencies are PCRE (http://www.pcre.org/) and zlib
-(http://zlib.net/).
-
-
-contribute
-----------
-
-If you have written any small but useful programs to deal with FASTQ files,
-please consider submitting them for inclusion in fastq-tools. Check out the
-Github page (https://github.com/dcjones/fastq-tools) or send mail to the author
-(dcjones@cs.washington.edu).
-
-
-copying
--------
-
-This package is provided under a permissive MIT-style license. In particular:
-
-Copyright (C) 2011 by Daniel C. Jones <dcjones@cs.washington.edu>
-
-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.
-
-

diff --git a/README.md b/README.md
new file mode 100644 (file)
index 0000000..75a28d3
--- /dev/null
+++ b/README.md
@@ -0,0 +1,77 @@
+
+fastq-tools
+===========
+
+This package provides a number of small and efficient programs to perform common
+tasks with high throughput sequencing data in the FASTQ format. All of the
+programs work with typical FASTQ files as well as gzipped FASTQ files.
+
+
+index
+-----
+
+The following programs are provided. See the individual man pages for more
+information.
+
+
+* *fastq-grep* : match sequences against regular expressions
+
+* *fastq-kmers* : count k-mer occurrences
+
+* *fastq-match* : (smith-waterman) local sequence alignment
+
+* *fastq-qual* : tabulate quality scores
+
+* *fastq-sample* : randomly sample reads, with or without replacement
+
+* *fastq-uniq* : count duplicate reads
+
+
+
+install
+-------
+
+On most systems, installation is as simple as `./configure && make install`.
+
+If the source was obtained from the git repository, the included `./autogen.sh`
+script must be run first to generate the `configure` script.
+
+The only external dependencies are PCRE (http://www.pcre.org/) and zlib
+(http://zlib.net/).
+
+
+contribute
+----------
+
+If you have written any small but useful programs to deal with FASTQ files,
+please consider submitting them for inclusion in fastq-tools. Check out the
+Github page (https://github.com/dcjones/fastq-tools) or send mail to the author
+(dcjones@cs.washington.edu).
+
+
+copying
+-------
+
+This package is provided under a permissive MIT-style license. In particular:
+
+Copyright (C) 2011 by Daniel C. Jones <dcjones@cs.washington.edu>
+
+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.
+
+