simple_bam_parser

A simple BAM file parser

BAM is the binary version of a SAM file. BAM is space efficient and allows fast random access, but not easy to parse like a ASCII based SAM file. Luckily libraries such as htslib exists. Yet, the documentation is minimal that for a beginner it takes time to get familiar with. Here are few simple programs that explains how to use those functions in htslib

At the moment there are 3 example programs :

1. randomaccess : A simple program that uses htslib to perform random access to a BAM file.

• Opens a sorted BAM file and its index, then
• Extracts and prints the reads aligned to the genomic region provided as a command line argument

2. sequentialaccess : A simple program that performs sequential access of a bam file

• Opens a BAM file
• Print the reads to the standard output

3. write : A simple program that make a copy of a BAM file

• Opens a BAM file
• Read read abd read and write to another BAM file

The source files are

• randomacess.c : source code for 1

• sequentialaccess.c : source code for 2

• write.c : source code for 3

• common.h and common.c : common functions used in example programs

Running

First clone the repository

git clone https://github.com/hasindu2008/simple_bam_parser.git

I have put a copy of htslib. Build it by the following command.

cd simple_bam_parser/htslib && make clean && ./configure && make

Then build the example programs

cd .. && make

Then run a program that you wish,

./randomacess input.bam chr:start_pos-stop_pos 
./sequentialaccess input.bam
./write input.bam output.bam

Some examples :

./randomacess test/sample.bam 1:10000-10005
./sequentialaccess test/sample.bam
./write test/sample.bam out.bam