Closed rgate closed 6 years ago
I think there is a syntax discrepancy between either Julia versions or Bio.jl versions and I can't figure out which is correct
tried following example on https://github.com/BioJulia/Bio.jl/blob/master/docs/src/man/alignments.md
julia> reader = open(BAM.Reader, bam_input) ERROR: UndefVarError: BAM not defined
but this seems to work julia> reader = open(BAMReader, bam_input) Bio.Align.BAMReader{IOStream}: header keys: SQ, PG, HD number of contigs: 8
and if I run this example command I get an error, but not sure where to help it find "BAM" julia> for record in reader
record
if BAM.ismapped(record) # print mapped position println(BAM.refname(record), ':', BAM.position(record)) end end
ERROR: UndefVarError: BAM not defined
Goal: I'd like to be able to extract the read name and sequence from each read and substring the sequence. thank you!
change "BAM" to "Bio.Align"
I think there is a syntax discrepancy between either Julia versions or Bio.jl versions and I can't figure out which is correct
tried following example on https://github.com/BioJulia/Bio.jl/blob/master/docs/src/man/alignments.md
julia> reader = open(BAM.Reader, bam_input) ERROR: UndefVarError: BAM not defined
but this seems to work julia> reader = open(BAMReader, bam_input) Bio.Align.BAMReader{IOStream}: header keys: SQ, PG, HD number of contigs: 8
and if I run this example command I get an error, but not sure where to help it find "BAM" julia> for record in reader
record
is a BAM.Record objectERROR: UndefVarError: BAM not defined
Goal: I'd like to be able to extract the read name and sequence from each read and substring the sequence. thank you!