From 5da017052b32433ecbd41042600271e7e0c4a387 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ciar=C3=A1n=20O=27Mara?= <Ciaran.OMara@utas.edu.au>
Date: Sun, 23 Feb 2020 14:43:34 +1100
Subject: [PATCH] Add messages to assertions

---
 src/bam/overlap.jl | 4 +++-
 src/bam/writer.jl  | 2 +-
 src/sam/flags.jl   | 3 +--
 src/sam/record.jl  | 2 +-
 4 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/bam/overlap.jl b/src/bam/overlap.jl
index e6212ed..fb28b1f 100644
--- a/src/bam/overlap.jl
+++ b/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)
         return nothing
diff --git a/src/bam/writer.jl b/src/bam/writer.jl
index 2460b3f..81bdf23 100644
--- a/src/bam/writer.jl
+++ b/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
diff --git a/src/sam/flags.jl b/src/sam/flags.jl
index 7b476fa..ded0df1 100644
--- a/src/sam/flags.jl
+++ b/src/sam/flags.jl
@@ -16,7 +16,7 @@ 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)
     docstring = """    $sym
     SAM/BAM flag: $doc
@@ -27,4 +27,3 @@ for (name, bits, doc) in [
         @doc $(docstring) const $(sym) = $(bits)
     end
 end
-
diff --git a/src/sam/record.jl b/src/sam/record.jl
index b241687..ef8bb6d 100644
--- a/src/sam/record.jl
+++ b/src/sam/record.jl
@@ -494,7 +494,7 @@ 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')