<commit_before>indelMINER
==========

Identify indels from BAM files.

## REQUIREMENTS
indelMINER should work on any standard 64 bit Linux environment with 

- GCC
- zlib (http://zlib.net)

## ACKNOWLEDGEMENTS
indelMINER uses Paul Hsieh's Superfasthash (http://www.azillionmonkeys.com/qed/hash.html) hash function. The hash function is encapsulated in the source file superfasthash.c within this distribution.

## SUMMARY
indelMINER refers to a set of algorithms to identify indels from whole genome 
resequencing datasets using paired-end reads. indelMINER uses a split-read 
approach to identify the precise breakpoints for indels of size less than a user
specified threshold, and supplements that with a paired-end approach to identify 
larger variants that are frequently missed with the split-read approach. 

## INSTALLATION
indelMINER uses the SAMtools (http://samtools.sourceforge.net) API to 
manipulate files in the BAM (Binary Alignment/Mapping) format. 

Please add the full path of your SAMtools installation to the Makefile in the 
distribution folder. For example, If your SAMtools installation is at 
/home/foo/samtools-0.1.18, then please replace the lines

INCDIR = 
LNKDIR = 

with the following in the Makefile

INCDIR = /home/foo/samtools-0.1.18
LNKDIR = /home/foo/samtools-0.1.18

Then, type:

make 

This should create an binary named indelminer in the "src" folder. Add the "src"
folder to your PATH or use the full path to the binay when running indelMINER

## TEST-DATASET<commit_msg>Made changes to README.<commit_after>indelMINER
==========

Identify indels from BAM files.

## REQUIREMENTS
indelMINER should work on any standard 64 bit Linux environment with 

- GCC
- zlib (http://zlib.net)

## ACKNOWLEDGEMENTS
indelMINER uses Paul Hsieh's Superfasthash (http://www.azillionmonkeys.com/qed/hash.html) hash function. The hash function is encapsulated in the source file superfasthash.c within this distribution.

## SUMMARY
indelMINER refers to a set of algorithms to identify indels from whole genome 
resequencing datasets using paired-end reads. indelMINER uses a split-read 
approach to identify the precise breakpoints for indels of size less than a user
specified threshold, and supplements that with a paired-end approach to identify 
larger variants that are frequently missed with the split-read approach. 

## INSTALLATION
indelMINER uses the SAMtools (http://samtools.sourceforge.net) API to 
manipulate files in the BAM (Binary Alignment/Mapping) format. 

Please add the full path of your SAMtools installation to the Makefile in the 
distribution folder. For example, If your SAMtools installation is at 
/home/foo/samtools-0.1.18, then please replace the lines
```
INCDIR = 
LNKDIR = 
```
with the following in the Makefile
```
INCDIR = /home/foo/samtools-0.1.18
LNKDIR = /home/foo/samtools-0.1.18
```
Then, type:
```
make 
```
This should create an binary named indelminer in the "src" folder. Add the "src"
folder to your PATH or use the full path to the binay when running indelMINER

## TEST-DATASET
{'fraction_non_alphanumeric': 0.06988188976377953, 'fraction_numerical': 0.009186351706036745, 'mean_word_length': 4.434937611408199, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, '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': '690977', 'n_tokens_mistral': 974, 'n_tokens_neox': 900, 'n_words': 386}