Updating a file random acess in bowwow dating 2016
In order to write and read String, we will be using method, which reads String in modified UTF-8 format.Though, in this program, I have closed file in try block, you should always do that in a finally block with additional try block, or better use try-with-resource statement from Java 7.It's similar to array data structure, Just like you can access any element in array by index you can read any content from file by using file pointer.A random access file actually behaves like a large array of bytes stored in file system and that's why its very useful for low latency applications which needs some kind of persistence e.g.
Then to obtain a specific read, you'd calculate the block number it'll appear in, decompress the block, and return the appropriate read.
It is indeed a very useful class from traditional Java IO API, which was only source of doing high speed IO before Java NIO came with memory mapped file.
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I would prefer a solution that does not require any extra files such as for example a reference genome.
The title of this question mentions a FASTQ only because FASTQ is a common format for storing unaligned reads on disk.If more than one record is to be retrieved, then the index needs to be stored in memory, perhaps with a framework such as pysam or htslib.