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fqme's Introduction

FASTQ ME

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Please do not use this for any serious work until unit tests have been completed

Quickstart

Compress and index (two-ways) the FASTQ with bgzip:

cat test.fastq | fqme index --output test.fastq.gz.fqi -n 100 | bgzip -c -i --index-name test.fastq.gz.gzi > test.fastq.gz

Extract entries:

fqme extract --input test.fastq.gz -s 100 -e 102

Help

fqme --help

To Build

cargo build --release

The executable is located in:

target/release/fqme

To Test

cargo test

fqme's People

Contributors

nh13 avatar sjackman avatar sstadick avatar

Stargazers

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Watchers

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Forkers

sstadick sjackman

fqme's Issues

Extract: decompress all the blocks on the fly

Currently we read in all the required bgzf blocks, then decompress them, storing all the decompressed data in a buffer. The entire buffer is then parsed into FASTQ records.

Instead, we could write a little reader class that only reads in a block and decompresses it as need. This would only require at most to uncompressed blocks of buffer in memory at any given time.

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