SAM parser

[bdeonovic]

I tried reading a sam file:

julia> reader = open(SAMReader, "1to2k.sam")
ERROR: AssertionError: upanchor! called with no anchor set
 in upanchor! at /Users/bdeonovic/.julia/v0.5/Bio/src/Ragel.jl:33 [inlined]
 in macro expansion at /Users/bdeonovic/.julia/v0.5/Bio/src/Ragel.jl:104 [inlined]
 in macro expansion at /Users/bdeonovic/.julia/v0.5/Bio/src/align/hts/sam/parser.jl:1299 [inlined]
 in _read!(::Bio.Align.SAMReader, ::Bio.Ragel.State{BufferedStreams.BufferedInputStream{IOStream}}, ::Bio.Align.SAMRecord) at /Users/bdeonovic/.julia/v0.5/Bio/src/Ragel.jl:182
 in read(::Bio.Align.SAMReader) at /Users/bdeonovic/.julia/v0.5/Bio/src/Ragel.jl:228
 in Bio.Align.SAMReader(::BufferedStreams.BufferedInputStream{IOStream}) at /Users/bdeonovic/.julia/v0.5/Bio/src/align/hts/sam/reader.jl:20
 in #open#2(::Array{Any,1}, ::Function, ::Type{Bio.Align.SAMReader}, ::String) at /Users/bdeonovic/.julia/v0.5/Bio/src/IO.jl:58
 in open(::Type{Bio.Align.SAMReader}, ::String) at /Users/bdeonovic/.julia/v0.5/Bio/src/IO.jl:58

However, after converting the SAM to BAM and using the BAMReader I had no problem reading the file.

[TransGirlCodes]

With any luck this will go away when we don't use Ragel anymore?

[bicycle1885]

@bdeonovic Can you paste the file or upload a part of it somewhere?

[bdeonovic]

Here is a small version of that sam file (same header + first few entries):

https://www.dropbox.com/s/gac7ni5yrmojoic/small.sam?dl=0

[bicycle1885]

@bdeonovic Thank you! I've fixed the bug in #377. This happens when reading a SAM file with large header section. The cause is in interactions between Ragel and BufferedStreams.jl.