Add messages to assertions

TODO: determine whether these assertions are intended for debugging purposes?

src/bam/overlap.jl

@@ -50,7 +50,9 @@ function Base.iterate(iter::OverlapIterator)
     if refindex === nothing
         throw(ArgumentError("sequence name $(iter.refname) is not found in the header"))
     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)
     if !isempty(chunks)
         seek(iter.reader, first(chunks).start)

src/bam/writer.jl

@@ -37,7 +37,7 @@ function Base.write(writer::Writer, record::Record)
 end
 
 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
 
     # magic bytes

src/sam/flags.jl

@@ -16,11 +16,10 @@ for (name, bits, doc) in [
         (:QCFAIL,        UInt16(0x200), "QC failure"                                                                ),
         (:DUP,           UInt16(0x400), "optical or PCR duplicate"                                                  ),
         (:SUPPLEMENTARY, UInt16(0x800), "supplementary alignment"                                                   ),]
-    @assert bits isa UInt16
+    @assert bits isa UInt16 "The bits must be of type UInt16."
     sym = Symbol("FLAG_", name)
     doc = string(@sprintf("0x%04x: ", bits), doc)
     @eval begin
         @doc $(doc) const $(sym) = $(bits)
     end
 end
-

src/sam/record.jl

@@ -499,7 +499,7 @@ function Base.getindex(record::Record, tag::AbstractString)
     end
 
     if typ == UInt8('A')
-        @assert lo == hi
+        @assert lo == hi "Values lo and hi must be equivalent."
         return Char(record.data[lo])
     end
     if typ == UInt8('i')