[Samtools-help] Extracting region as fasta

[John C. <cr...@gm...>]

>From a bam file I'd like to extract the alignment, for each aligning read,
corresponding to the 10 bp region contig1:100-109 of the read, writing it
as fasta. This would produce something like

>1/1
ACGTACGTAC
>20/1
ACGTAC-TAC
>22/1
C-GTACG-AC
 . . .

It seemed a combo of "samtools view ... contig1:100-109" and "samtools
fasta" would do the trick but I haven't had luck with it yet. Any
suggestions?