samtools --version
samtools 1.2-2-gf8a6274
Using htslib 1.2.1
Copyright (C) 2015 Genome Research Ltd.
$ samtools view foo.cram ref0:100-100
read.96 16 ref0 97 40 4M * 0 0 GTAG IIII MD:Z:4 NM:i:0
read.97 16 ref0 98 40 4M * 0 0 TAGG IIII MD:Z:4 NM:i:0
read.98 16 ref0 99 40 4M * 0 0 AGGT IIII MD:Z:4 NM:i:0
read.99 16 ref0 100 40 4M * 0 0 GGTG IIII MD:Z:4 NM:i:0
If the reference range is given such that end == (start -1) the range is accepted. This should fail:
$ samtools view foo.cram ref0:100-99
read.96 16 ref0 97 40 4M * 0 0 GTAG IIII MD:Z:4 NM:i:0
read.97 16 ref0 98 40 4M * 0 0 TAGG IIII MD:Z:4 NM:i:0
read.98 16 ref0 99 40 4M * 0 0 AGGT IIII MD:Z:4 NM:i:0
The following fails (as do smaller values of end), but with a spurious error message:
$ samtools view foo.cram ref0:100-98
[main_samview] region "ref0:100-98" specifies an unknown reference name. Continue anyway.
If the reference range is given such that
end == (start -1)the range is accepted. This should fail:The following fails (as do smaller values of
end), but with a spurious error message: