glactools ALWAYS prints compressed binary. The only thing to modify is the ability to print as uncompressed binary (-u option), this is recommended when using UNIX pipes. However if you wish to view an ACF/GLF a
Unfortunately, the tabix maintainers did not include an install target in their Makefile so you cannot just run make install and have everything deposited where you need it. Because of this, it is recommended that you copy bgzip somewhere in your $PATH so it is convenient to use /usr/...
There is also support for indexing FASTA files with multiple entries through fai_index. This indexing enables a faster reading of a particular FASTA entry without having to read through the file starting from the beginning. Starting from version 2.3.X SeqAn also supports using BAM to store ...
Due to the need for querying the compressed file twice and an additional scan (thegrepcall to find the header, involving examination of the entire guessed space), this solution is not optimal. Refer to the following section to understand the significant slowness ofbzip2. Perspective Considering th...
In general, whenever multiple VCFs are ## read simultaneously, they must be indexed and therefore also ## compressed. (Note that files with non-standard index names can be ## accessed as e.g. "bcftools view -r X:2928329 ## file.vcf.gz##idx##non-standard-index-name".) ## ## ...