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Small general purpose library for C and Python with focus on bioinformatics.
C Python C++ Makefile HTML Shell

Merge pull request #23 from ifiddes/master

found bug in fastaRead where lack of trailing newline leads to truncation
latest commit db59f3a8ed
@joelarmstrong joelarmstrong authored
Failed to load latest commit information.
C Merge branch 'development' of https://github.com/benedictpaten/sonLib
doc Added install doc
externalTools Restoring the custom verbosity that we added to CuTest.
.gitignore reverting back to pre include.mk.tmpl status. This file is included b…
LICENSE.txt Test commit.
Makefile making the Makefile more awesome.
README.md Making the readme nicer
__init__.py changing copyright date from 2011 to 2012
allTests.py removing the redundant run of the unit tests
bioio.py oops
bioioTest.py Adding fastq functions
cigarsTest.py changing copyright date from 2011 to 2012
include.mk Removing the " -stdlib=libstdc++" from the sonLib include file, which
kvdbTest.py Disabling test of mysql database interface, as it's broken and we
misc.py changing copyright date from 2011 to 2012
nxnewick.py Make adding implied root nodes optional to fix tests
nxnewickTest.py Make adding implied root nodes optional to fix tests
nxtree.py add reroot function to nxtree, needed by new outgroup logic, and fix …
nxtreeTest.py add reroot function to nxtree, needed by new outgroup logic, and fix …
setup.py Fixing build vs. build_py bug; build command is never actually used
sonLib_daemonize.py add spanwDaemon() method to bioio.py, which calls new script
tree.py changing copyright date from 2011 to 2012
treeTest.py changing copyright date from 2011 to 2012
unitTest.py changing copyright date from 2011 to 2012

README.md

sonLib

sonLib is a compact C/Python library for sequence analysis in bioinformatics.

(c) 2006 - 2012 The Author(s). See LICENSE.txt for details.

Author

Benedict Paten

Description

For basic data-structures in C it contains:

  • array lists (automatically resizing)
  • hashes
  • sets (backed by hashes)
  • sorted sets (backed by an AVL tree)
  • containers (for putting primitives into the above data-structures)
  • better string functions
  • simple exception mechanism
  • logging functions

For bioinformatic data-structures it contains (or will contain):

  • Fasta I/O functions
  • MAF I/O functions
  • Newick tree I/O functions

For more details see the Full README in doc/README

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