Thanks Colin. In fact I used bgzip to compress data (saving space). It just seems that I don't need the gzi index and I wonder in which case this file is used.
Le 08/03/2017 à 16:42, Colin a écrit : > Technically you can get random access without using bgzip on the fasta file > > You can just do "samtools faidx plainfasta.fa" and the plain text > fasta+fasta index(fai) allows random access. > > I can't comment on why both gzi and fai are both necessary in the > bgzip case though! > > -Colin > > On Tue, Mar 7, 2017 at 3:13 AM, sebastien letort > <sebastien.let...@irisa.fr <mailto:sebastien.let...@irisa.fr>> wrote: > > Hi, > > Only for my comprehension. > > I've got a fasta file (many short sequences) that I compressed with > bgzip to grant random access. > I wrote a tiny code in python (with pysam) that parse my file. > > I've noticed that a myfile.gz.fai has been generated whereas I already > had a myfile.gzi file index. > > Does that means gzi index is not the index to use with fasta file ? > For what purpose gzi file is dedicated ? > > Regards, > Sébastien > > > ------------------------------------------------------------------------------ > Announcing the Oxford Dictionaries API! The API offers world-renowned > dictionary content that is easy and intuitive to access. Sign up for an > account today to start using our lexical data to power your apps and > projects. Get started today and enter our developer competition. > http://sdm.link/oxford > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > <mailto:Samtools-help@lists.sourceforge.net> > https://lists.sourceforge.net/lists/listinfo/samtools-help > <https://lists.sourceforge.net/lists/listinfo/samtools-help> > > ------------------------------------------------------------------------------ Announcing the Oxford Dictionaries API! The API offers world-renowned dictionary content that is easy and intuitive to access. Sign up for an account today to start using our lexical data to power your apps and projects. Get started today and enter our developer competition. http://sdm.link/oxford _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
