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Add messages to assertions

This commit is contained in:
Ciarán O'Mara 2020-02-23 14:43:34 +11:00
parent 8424757cc2
commit 5da017052b
4 changed files with 6 additions and 5 deletions

View file

@ -50,7 +50,9 @@ function Base.iterate(iter::OverlapIterator)
if refindex === nothing if refindex === nothing
throw(ArgumentError("sequence name $(iter.refname) is not found in the header")) throw(ArgumentError("sequence name $(iter.refname) is not found in the header"))
end end
@assert iter.reader.index !== nothing
@assert iter.reader.index !== nothing "Reader index cannot be nothing."
chunks = Indexes.overlapchunks(iter.reader.index.index, refindex, iter.interval) chunks = Indexes.overlapchunks(iter.reader.index.index, refindex, iter.interval)
if isempty(chunks) if isempty(chunks)
return nothing return nothing

View file

@ -37,7 +37,7 @@ function Base.write(writer::Writer, record::Record)
end end
function write_header(stream, header, refseqnames, refseqlens) function write_header(stream, header, refseqnames, refseqlens)
@assert length(refseqnames) == length(refseqlens) @assert length(refseqnames) == length(refseqlens) "Lengths of refseq names and lengths must match."
n = 0 n = 0
# magic bytes # magic bytes

View file

@ -16,7 +16,7 @@ for (name, bits, doc) in [
(:QCFAIL, UInt16(0x200), "QC failure" ), (:QCFAIL, UInt16(0x200), "QC failure" ),
(:DUP, UInt16(0x400), "optical or PCR duplicate" ), (:DUP, UInt16(0x400), "optical or PCR duplicate" ),
(:SUPPLEMENTARY, UInt16(0x800), "supplementary alignment" ),] (:SUPPLEMENTARY, UInt16(0x800), "supplementary alignment" ),]
@assert bits isa UInt16 @assert bits isa UInt16 "The bits must be of type UInt16."
sym = Symbol("FLAG_", name) sym = Symbol("FLAG_", name)
docstring = """ $sym docstring = """ $sym
SAM/BAM flag: $doc SAM/BAM flag: $doc
@ -27,4 +27,3 @@ for (name, bits, doc) in [
@doc $(docstring) const $(sym) = $(bits) @doc $(docstring) const $(sym) = $(bits)
end end
end end

View file

@ -494,7 +494,7 @@ function Base.getindex(record::Record, tag::AbstractString)
end end
if typ == UInt8('A') if typ == UInt8('A')
@assert lo == hi @assert lo == hi "Values lo and hi must be equivalent."
return Char(record.data[lo]) return Char(record.data[lo])
end end
if typ == UInt8('i') if typ == UInt8('i')