FASTA alignment index retrieval

[kullrich]

Dear samtools, I am working with FASTA alignments, which have different sequence names (aka chromosomes) but all of the same length. No I needed to create a wrapper around samtools faidx to retrieve and append the single sequences into one output region (loop over all names in "cut -f 1 xxx.fai"; for each NAME do a faidx xxx.fa NAME:REGION"). Would it be possible to write a new function within faidx to extract the same REGION for all sequences in an indexed FASTA file? One would first need to check in the .fai file if all are the same length, if this is true one can go on and extract the same region in a while loop. Thank you in anticipation Kristian Ullrich