Welcome to VCFPy’s documentation!¶

Stable release¶

To install vcfpy, run this command in your terminal:

$ pip install vcfpy

This is the preferred method to install VCFPy, as it will always install the most recent stable release.

If you don’t have pip installed, this Python installation guide can guide you through the process.

From sources¶

The sources for vcfpy can be downloaded from the Github repo.

You can either clone the public repository:

$ git clone git://github.com/bihealth/vcfpy

Or download the tarball:

$ curl  -OL https://github.com/bihealth/vcfpy/tarball/master

Once you have a copy of the source, you can install it with:

$ python setup.py install

Reading VCF Files¶

The following is an example for reading VCF files and writing out a TSV file with the genotype calls of all SNVs. You can find the example Python and VCF file in the sources below the directory examples/vcf_to_tsv.

#!/usr/bin/env python
# -*- coding: utf-8 -*-
import vcfpy

# Open file, this will read in the header
reader = vcfpy.Reader.from_path('input.vcf')

# Build and print header
header = ['#CHROM', 'POS', 'REF', 'ALT'] + reader.header.samples.names
print('\t'.join(header))

for record in reader:
    if not record.is_snv():
        continue
    line = [record.CHROM, record.POS, record.REF]
    line += [alt.value for alt in record.ALT]
    line += [call.data.get('GT') or './.' for call in record.calls]
    print('\t'.join(map(str, line)))

The program call looks as follows.

$ ./vcf_to_tsv.py
#CHROM	POS	REF	ALT	BLANK	NA12878	NA12891	NA12892	NA19238	NA19239	NA19240
chr22	42522392	G	A	0/0	0/1	0/1	0/0	0/0	0/0	0/0
chr22	42522597	C	T	0/1	0/0	0/0	0/0	0/0	0/0	0/0
chr22	42522613	G	C	0/1	0/1	0/0	0/1	0/1	0/1	0/1
chr22	42523003	A	G	0/1	1/1	0/1	0/1	0/1	0/1	0/1
chr22	42523209	T	C	0/1	1/1	0/1	0/1	0/1	0/1	0/1
chr22	42523211	T	C	0/0	0/1	0/1	0/0	0/0	0/0	0/0
chr22	42523409	G	T	0/1	0/1	0/0	0/1	0/1	0/1	0/1
chr22	42523491	C	T	0/1	0/0	0/0	0/0	0/0	0/0	0/0
chr22	42523507	A	G	0/1	0/0	0/0	0/0	0/0	0/0	0/0
chr22	42523805	C	T	0/0	0/0	0/1	0/0	0/0	0/0	0/0
chr22	42523943	A	G	0/1	1/1	0/1	0/1	0/1	0/1	0/1
chr22	42524435	T	A	0/1	0/0	0/0	0/0	0/0	0/1	0/1
[...]

Writing VCF Files¶

The following shows how to add values to the FILTER column to records of an existing VCF file. Adding to existing records is simpler than constructing them from scratch, of course.

#!/usr/bin/env python
# -*- coding: utf-8 -*-
import vcfpy

# Open input, add FILTER header, and open output file
reader = vcfpy.Reader.from_path('input.vcf')
reader.header.add_filter_line(vcfpy.OrderedDict([
    ('ID', 'DP10'), ('Description', 'total DP < 10')]))
writer = vcfpy.Writer.from_path(
    '/dev/stdout', reader.header, reader.samples)

# Add "DP10" filter to records having less than 10 reads
for record in reader:
    ad = sum(c.data.get('DP', 0) for c in record.calls)
    if ad < 10:
        record.add_filter('DP10')
    writer.write_record(record)

The program call looks as follows.

##fileformat=VCFv4.3
##contig=<ID=20,length=62435964>
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
##FILTER=<ID=DP10,Description="total DP < 10">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
20	14370	rs6054257	G	A	29	PASS	NS=3;DP=14;AF=0.5;DB;H2	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
20	17330	.	T	A	3	q10	NS=3;DP=11;AF=0.017	GT:GQ:DP:HQ	0|0:49:3:58,50	0|1:3:5:65,3	0/0:41:3:40,30
20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4:40,30
20	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2:40,30
20	1234567	microsat1	GTC	G,GTCT	50	PASS;DP10	NS=3;DP=9;AA=G	GT:GQ:DP	0/1:35:4	0/2:17:2	1/1:40:3

Jumping in Tabix-indexed Files¶

The following shows a small program that extracts a genomic region from the input VCF file and writes it to stdout.

#!/usr/bin/env python
# -*- coding: utf-8 -*-
import vcfpy

# Open input, add FILTER header, and open output file
reader = vcfpy.Reader.from_path('input.vcf.gz')
writer = vcfpy.Writer.from_path(
    '/dev/stdout', reader.header, reader.samples)

# Fetch region 20:1,110,694-1,230,237.  Note that the coordinates
# in the API call are zero-based and describe half-open intervals.
for record in reader.fetch('20', 1110695, 1230237):
    writer.write_record(record)

The program call looks as follows.

##fileformat=VCFv4.3
##fileDate=20090805
##source=myImputationProgramV3.1
##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=20,length=62435964>
##phasing=partial
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10;AF=0.333,0.667;AA=T;DB	GT:GQ:DP:HQ1|2:21:6:23,27	2|1:2:0:18,2	2/2:35:4:40,30
20	1230237	.	T	.	47	PASS	NS=3;DP=13;AA=T	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2:40,30

Keep Input Verbatim Where Possible¶

Try to keep the input verbatim if there is no strong reason for adjusting it. Strong reasons include fixing Type or Number in header lines describing arrays of strings, for example.

Whenever possible, keep the header order intact. VCFPy does this automatically for you (in contrast to PyVCF).

Prefer Soft-Filters over Hard-Filters¶

Soft-filters mean annotating your VCF records in the FILTER column whereas Hard-filters mean removing records from VCF file. In many situations, it is useful to keep around all VCF records and just annotate why they are to be dropped. Then, in the last step, only the interesting ones are kept.

This makes tracing back easier when and why a record was removed.

vcfpy.OrderedDict¶

Convenience export of OrderedDict. When available, the cyordereddict, a Cython-reimplementation of OrderedDict is used for Python before 3.5 (from 3.5, Python ships with a fast, C implementation of OrderedDict).

class vcfpy.OrderedDict¶

Dictionary that remembers insertion order

clear() → None. Remove all items from od.¶

copy() → a shallow copy of od¶

fromkeys(S[, v]) → New ordered dictionary with keys from S.¶

If not specified, the value defaults to None.

items() → a set-like object providing a view on D's items¶

keys() → a set-like object providing a view on D's keys¶

move_to_end()¶

Move an existing element to the end (or beginning if last==False). Raises KeyError if the element does not exist. When last=True, acts like a fast version of self[key]=self.pop(key).

pop(k[, d]) → v, remove specified key and return the corresponding¶

value. If key is not found, d is returned if given, otherwise KeyError is raised.

popitem() → (k, v), return and remove a (key, value) pair.¶

Pairs are returned in LIFO order if last is true or FIFO order if false.

setdefault(k[, d]) → od.get(k,d), also set od[k]=d if k not in od¶

update([E, ]**F) → None. Update D from mapping/iterable E and F.¶

If E present and has a .keys() method, does: for k in E: D[k] = E[k] If E present and lacks .keys() method, does: for (k, v) in E: D[k] = v In either case, this is followed by: for k, v in F.items(): D[k] = v

values() → an object providing a view on D's values¶

vcfpy.Header¶

class vcfpy.Header(lines=[], samples=None)[source]¶

Represent header of VCF file

While this class allows mutating records, it should not be changed once it has been assigned to

This class provides function for adding lines to a header and updating the supporting index data structures. There is no explicit API for removing header lines, the best way is to reconstruct a new Header instance with a filtered list of header lines.

add_contig_line(mapping)[source]¶

Add “contig” header line constructed from the given mapping

add_filter_line(mapping)[source]¶

Add FILTER header line constructed from the given mapping

add_format_line(mapping)[source]¶

Add FORMAT header line constructed from the given mapping

add_info_line(mapping)[source]¶

Add INFO header line constructed from the given mapping

add_line(header_line)[source]¶

Add header line, updating any necessary support indices

filter_ids()[source]¶

Return list of all filter IDs

format_ids()[source]¶

Return list of all format IDs

get_format_field_info(key)[source]¶

Return FieldInfo for the given INFO field

get_info_field_info(key)[source]¶

Return FieldInfo for the given INFO field

get_lines(key)[source]¶

Return header lines having the given key as their type

info_ids()[source]¶

Return list of all info IDs

lines = None¶

list of :py:HeaderLine objects

samples = None¶

SamplesInfo object

vcfpy.HeaderLine¶

class vcfpy.HeaderLine(key, value)[source]¶

Base class for VCF header lines

key = None¶

str with key of header line

serialize()[source]¶

Return VCF-serialized version of this header line

vcfpy.header_without_lines¶

vcfpy.header_without_lines(header, remove)[source]¶

Return Header without lines given in remove

remove is an iterable of pairs key/ID with the VCF header key and ID of entry to remove. In the case that a line does not have a mapping entry, you can give the full value to remove.

vcfpy.SimpleHeaderFile¶

vcfpy.AltAlleleHeaderLine¶

class vcfpy.AltAlleleHeaderLine(key, value, mapping)[source]¶

Alternative allele header line

Mostly used for defining symbolic alleles for structural variants and IUPAC ambiguity codes

classmethod from_mapping(klass, mapping)[source]¶

Construct from mapping, not requiring the string value

id = None¶

name of the alternative allele

vcfpy.MetaHeaderLine¶

class vcfpy.MetaHeaderLine(key, value, mapping)[source]¶

Alternative allele header line

Used for defining set of valid values for samples keys

classmethod from_mapping(klass, mapping)[source]¶

Construct from mapping, not requiring the string value

id = None¶

name of the alternative allele

vcfpy.PedigreeHeaderLine¶

class vcfpy.PedigreeHeaderLine(key, value, mapping)[source]¶

Header line for defining a pedigree entry

classmethod from_mapping(klass, mapping)[source]¶

Construct from mapping, not requiring the string value

id = None¶

name of the alternative allele

vcfpy.SampleHeaderLine¶

class vcfpy.SampleHeaderLine(key, value, mapping)[source]¶

Header line for defining a SAMPLE entry

classmethod from_mapping(klass, mapping)[source]¶

Construct from mapping, not requiring the string value

id = None¶

name of the alternative allele

vcfpy.ContigHeaderLine¶

class vcfpy.ContigHeaderLine(key, value, mapping)[source]¶

Contig header line

Most importantly, parses the 'length' key into an integer

classmethod from_mapping(klass, mapping)[source]¶

Construct from mapping, not requiring the string value

id = None¶

name of the contig

length = None¶

length of the contig, None if missing

vcfpy.FilterHeaderLine¶

class vcfpy.FilterHeaderLine(key, value, mapping)[source]¶

FILTER header line

description = None¶

description for the filter, None if missing

classmethod from_mapping(klass, mapping)[source]¶

Construct from mapping, not requiring the string value

id = None¶

token for the filter

vcfpy.CompoundHeaderLine¶

class vcfpy.CompoundHeaderLine(key, value, mapping)[source]¶

Base class for compound header lines, currently format and header lines

Compound header lines describe fields that can have more than one entry.

mapping = None¶

OrderedDict with key/value mapping

vcfpy.InfoHeaderLine¶

class vcfpy.InfoHeaderLine(key, value, mapping)[source]¶

Header line for INFO fields

Note that the Number field will be parsed into an int if possible. Otherwise, the constants HEADER_NUMBER_* will be used.

description = None¶

description, should be given, None if not given

classmethod from_mapping(klass, mapping)[source]¶

Construct from mapping, not requiring the string value

id = None¶

key in the INFO field

source = None¶

source of INFO field, None if not given

type = None¶

value type

version = None¶

version of INFO field, None if not given

vcfpy.FormatHeaderLine¶

class vcfpy.FormatHeaderLine(key, value, mapping)[source]¶

Header line for FORMAT fields

description = None¶

description, should be given, None if not given

classmethod from_mapping(klass, mapping)[source]¶

Construct from mapping, not requiring the string value

id = None¶

key in the INFO field

source = None¶

source of INFO field, None if not given

type = None¶

value type

version = None¶

version of INFO field, None if not given

vcfpy.FieldInfo¶

class vcfpy.FieldInfo(type_, number)[source]¶

Core information for describing field type and number

number = None¶

Number description, either an int or constant

type = None¶

The type, one of INFO_TYPES or FORMAT_TYPES

vcfpy.SamplesInfos¶

class vcfpy.SamplesInfos(sample_names)[source]¶

Helper class for handling and mapping of sample names to numeric indices

name_to_idx = None¶

mapping from sample name to index

names = None¶

list of sample names

vcfpy.Reader¶

vcfpy.Writer¶

vcfpy.VCFPyException¶

exception vcfpy.VCFPyException[source]¶

Base class for module’s exception

vcfpy.InvalidHeaderException¶

exception vcfpy.InvalidHeaderException[source]¶

Raised in the case of invalid header formatting

vcfpy.InvalidRecordException¶

exception vcfpy.InvalidRecordException[source]¶

Raised in the case of invalid record formatting

vcfpy.IncorrectVCFFormat¶

exception vcfpy.IncorrectVCFFormat[source]¶

Raised on problems parsing VCF

vcfpy.HeaderNotFound¶

exception vcfpy.HeaderNotFound[source]¶

Raised when a VCF header could not be found

vcfpy.Record¶

class vcfpy.Record(CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, calls)[source]¶

Represent one record from the VCF file

Record objects are iterators of their calls

ALT = None¶

A list of alternative allele records of type AltRecord

CHROM = None¶

A str with the chromosome name

FILTER = None¶

A list of strings for the FILTER column

FORMAT = None¶

A list of strings for the FORMAT column

ID = None¶

A list of the semicolon-separated values of the ID column

INFO = None¶

An OrderedDict giving the values of the INFO column, flags are mapped to True

POS = None¶

An int with a 1-based begin position

QUAL = None¶

The quality value, can be None

REF = None¶

A str with the REF value

add_filter(label)[source]¶

Add label to FILTER if not set yet

add_format(key, value=None)[source]¶

Add an entry to format

The record’s calls data[key] will be set to value if not yet set and value is not None. If key is already in FORMAT then nothing is done.

affected_end¶

Return affected start position in 0-based coordinates

For SNVs, MNVs, and deletions, the behaviour is based on the start position and the length of the REF. In the case of insertions, the position behind the insert position is returned, yielding a 0-length interval together with :py:method:`affected_start`

affected_start¶

Return affected start position in 0-based coordinates

For SNVs, MNVs, and deletions, the behaviour is the start position. In the case of insertions, the position behind the insert position is returned, yielding a 0-length interval together with :py:method:`affected_end`

begin = None¶

An int with a 0-based begin position

call_for_sample = None¶

A mapping from sample name to entry in self.calls

calls = None¶

A list of genotype Call objects

end = None¶

An int with a 0-based end position

is_snv()[source]¶

Return True if it is a SNV

vcfpy.Call¶

class vcfpy.Call(sample, data, site=None)[source]¶

The information for a genotype callable

By VCF, this should always include the genotype information and can contain an arbitrary number of further annotation, e.g., the coverage at the variant position.

called = None¶

whether or not the variant is fully called

data = None¶

an OrderedDict with the key/value pair information from the call’s data

gt_alleles = None¶

the allele numbers (0, 1, ...) in this calls or None for no-call

gt_bases¶

Return the actual genotype alleles, e.g. if VCF genotype is 0/1, could return A/T

gt_phase_char()[source]¶

Return character to use for phasing

gt_type¶

The type of genotype, mapping is

• hom_ref = 0
• het = 1
• hom_alt = 2 (which alt is untracked)
• uncalled = None

is_filtered¶

Return True for filtered calls

is_het¶

Return True for filtered calls

is_phased¶

Return True for phased calls

is_variant¶

Return True for filtered calls

phased¶

Return boolean indicating whether this call is phased

plodity = None¶

the number of alleles in this sample’s call

sample = None¶

the name of the sample for which the call was made

site = None¶

the Record of this Call

vcfpy.AltRecord¶

class vcfpy.AltRecord(type_=None)[source]¶

An alternative allele Record

Currently, can be a substitution, an SV placeholder, or breakend

type = None¶

String describing the type of the variant, could be one of SNV, MNV, could be any of teh types described in the ALT header lines, such as DUP, DEL, INS, ...

vcfpy.Substitution¶

class vcfpy.Substitution(type_, value)[source]¶

A basic alternative allele record describing a REF->AltRecord substitution

Note that this subsumes MNVs, insertions, and deletions.

value = None¶

The alternative base sequence to use in the substitution

vcfpy.SV¶

class vcfpy.SV(type_, value)[source]¶

Code for structural variant allele

value = None¶

The alternative base sequence to use in the substitution

vcfpy.BreakEnd¶

class vcfpy.BreakEnd(type_, value)[source]¶

A placeholder for a breakend

value = None¶

The alternative base sequence to use in the substitution

vcfpy.SingleBreakEnd¶

class vcfpy.SingleBreakEnd(type_, value)[source]¶

A placeholder for a single breakend

value = None¶

The alternative base sequence to use in the substitution

vcfpy.SymbolicAllele¶

class vcfpy.SymbolicAllele(type_, value)[source]¶

A placeholder for a symbolic allele

value = None¶

The alternative base sequence to use in the substitution

Types of Contributions¶

Get Started!¶

Ready to contribute? Here’s how to set up vcfpy for local development.

1. Fork the vcfpy repo on GitHub.

2. Clone your fork locally:

   $ git clone git@github.com:your_name_here/vcfpy.git
   

3. Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:

   $ mkvirtualenv vcfpy
   $ cd vcfpy/
   $ python setup.py develop
   

4. Create a branch for local development:

   $ git checkout -b name-of-your-bugfix-or-feature
   

   Now you can make your changes locally.

5. When you’re done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox:

   $ flake8 vcfpy tests
   $ python setup.py test or py.test
   $ tox
   

   To get flake8 and tox, just pip install them into your virtualenv.

6. Commit your changes and push your branch to GitHub:

   $ git add .
   $ git commit -m "Your detailed description of your changes."
   $ git push origin name-of-your-bugfix-or-feature
   

7. Submit a pull request through the GitHub website.

Pull Request Guidelines¶

Before you submit a pull request, check that it meets these guidelines:

1. The pull request should include tests.
2. If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.rst.
3. The pull request should work for Python 3.3, 3.4 and 3.5. Check https://travis-ci.org/bihealth/vcfpy/pull_requests and make sure that the tests pass for all supported Python versions.

Tips¶

To run a subset of tests:

$ py.test tests.test_vcfpy

Development Lead¶

• Manuel Holtgrewe <manuel.holtgrewe@bihealth.de>

Contributors¶

None yet. Why not be the first?

HEAD¶

• Reader and Writer can now be used as context manager (with with)
• Including license in documentation, including Biopython license
• Adding support for writing bgzf files (taken from Biopython)
• Adding support for parsing arrays in header lines
• Removing example-4.1-bnd.vcf example file because v4.1 tumor derival lacks ID field
• Adding AltAlleleHeaderLine, MetaHeaderLine, PedigreeHeaderLine, and SampleHeaderLine
• Renaming SimpleHeaderFile to SimpleHeaderLine
• Warn on missing FILTER entries on parsing
• Reordered parameters in from_stream and from_file (#18)
• Renamed from_file to from_stream (#18)
• Renamed Reader.jump_to to Reader.fetch
• Adding header_without_lines function
• Generally extending API to make it esier to use
• Upgrading dependencies, enabling pyup-bot
• Greatly extending documentation

0.2.1 (2016-09-19)¶

• First release on PyPI

VCFPy License¶

You can find the License of VCFPy below.

MIT License

Copyright (c) 2016, Berlin Institute of Health

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.

Biopython License Agreement¶

The bgzf writing code is taken from the Biopython project. You can find a copy of the license below.

                Biopython License Agreement

Permission to use, copy, modify, and distribute this software and its
documentation with or without modifications and for any purpose and
without fee is hereby granted, provided that any copyright notices
appear in all copies and that both those copyright notices and this
permission notice appear in supporting documentation, and that the
names of the contributors or copyright holders not be used in
advertising or publicity pertaining to distribution of the software
without specific prior permission.

THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
OR PERFORMANCE OF THIS SOFTWARE.