<commit_before># basicfiltering
Basic Filtering for: 

1. Variant Allele Frequency = 1% (default)
2. Variant Reads = 5 (default)
3. Tumor-Normal Variant Allele Frequency Ratio >= 5  (default)
4. If vcf of hotspot location are given it skips positions that have hotspots regardless of not satisfying number `3` from the above criteria

for Multiple Tools

[![Build Status](https://travis-ci.org/rhshah/basicfiltering.svg?branch=master)](https://travis-ci.org/rhshah/basicfiltering)
[![Build Status](https://travis-ci.org/rhshah/basicfiltering.svg?branch=master)](https://travis-ci.org/rhshah/basicfiltering)

## Requirements:
- pyvcf : [v0.6.8](http://pyvcf.readthedocs.io/en/latest/INTRO.html)
- pandas : [v0.16.2](http://pandas.pydata.org/)
- nose : [v1.3.7](http://nose.readthedocs.io/en/latest/)
<commit_msg>Add Code Coverage badge<commit_after># basicfiltering
Basic Filtering for: 

1. Variant Allele Frequency = 1% (default)
2. Variant Reads = 5 (default)
3. Tumor-Normal Variant Allele Frequency Ratio >= 5  (default)
4. If vcf of hotspot location are given it skips positions that have hotspots regardless of not satisfying number `3` from the above criteria

for Multiple Tools

[![Build Status](https://travis-ci.org/rhshah/basicfiltering.svg?branch=master)](https://travis-ci.org/rhshah/basicfiltering)
[![codecov](https://codecov.io/gh/rhshah/basicfiltering/branch/master/graph/badge.svg)](https://codecov.io/gh/rhshah/basicfiltering)

## Requirements:
- pyvcf : [v0.6.8](http://pyvcf.readthedocs.io/en/latest/INTRO.html)
- pandas : [v0.16.2](http://pandas.pydata.org/)
- nose : [v1.3.7](http://nose.readthedocs.io/en/latest/)

{'fraction_non_alphanumeric': 0.1537522879804759, 'fraction_numerical': 0.021964612568639415, 'mean_word_length': 4.795053003533569, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 5, 'https://': 8, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1131188', 'n_tokens_mistral': 625, 'n_tokens_neox': 591, 'n_words': 126}