From 433b8d14e8e11735d4196b71bf29f83482cd3ebd Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ciara=CC=81n=20O=27Mara?= <Ciaran.OMara@utas.edu.au>
Date: Thu, 13 Aug 2020 16:45:51 +1000
Subject: [PATCH 1/2] Begin crosschecks

---
 test/runtests.jl        |  1 +
 test/test_crosscheck.jl | 54 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 55 insertions(+)
 create mode 100644 test/test_crosscheck.jl

diff --git a/test/runtests.jl b/test/runtests.jl
index 970c3a1..beede29 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -25,3 +25,4 @@ end
 
 include("test_sam.jl")
 include("test_bam.jl")
+include("test_crosscheck.jl")
diff --git a/test/test_crosscheck.jl b/test/test_crosscheck.jl
new file mode 100644
index 0000000..0e853ef
--- /dev/null
+++ b/test/test_crosscheck.jl
@@ -0,0 +1,54 @@
+@testset "Cross Check Properties" begin
+
+	Broadcast.broadcastable(x::XAM.BAM.Record) = Ref(x) #TODO: consider moving to XAM.jl.
+	Broadcast.broadcastable(x::XAM.SAM.Record) = Ref(x) #TODO: consider moving to XAM.jl
+
+	function crosscheck(bam::BAM.Record, sam::SAM.Record, property::Symbol)
+
+		bam_property = getproperty(XAM.BAM, property)
+		sam_property = getproperty(XAM.SAM, property)
+
+		if bam_property(bam) != sam_property(sam)
+			@warn "$property result is not the same" bam_property(bam) sam_property(sam)
+			return false
+		end
+
+		return true
+	end
+
+	samdir = path_of_format("SAM")
+	bamdir = path_of_format("BAM")
+
+	filenames = [
+		"ce#1",
+		"ce#2",
+		"ce#5",
+		"ce#5b",
+		"ce#unmap",
+		"ce#unmap1",
+		"ce#unmap2",
+	]
+
+	properties = [
+		:position,# POS
+		:tempname,# QNAME
+		:mappingquality,# MAPQ
+		:cigar, # CIGAR
+		:flag, # FLAG
+		:sequence, # SEQ
+		:nextposition, # PNEXT
+		:templength, # TLEN
+	]
+
+	for filename in filenames
+
+		records_bam = collect(open(BAM.Reader, joinpath(bamdir, filename * ".bam")))
+		records_sam = collect(open(SAM.Reader, joinpath(samdir, filename * ".sam")))
+
+		for (bam, sam) in zip(records_bam, records_sam)
+			@test all(crosscheck.(bam, sam, properties)) == true
+		end
+
+	end
+
+end # testset Crosscheck

From d38c2becf0dc15b27bd40237f313db74cae593b8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ciara=CC=81n=20O=27Mara?= <Ciaran.OMara@utas.edu.au>
Date: Thu, 13 Aug 2020 14:06:43 +1000
Subject: [PATCH 2/2] Minimal adjustements

---
 src/bam/record.jl |  5 ++++-
 src/sam/record.jl | 26 ++++++++++++++------------
 2 files changed, 18 insertions(+), 13 deletions(-)

diff --git a/src/bam/record.jl b/src/bam/record.jl
index a70bb17..ad911b4 100644
--- a/src/bam/record.jl
+++ b/src/bam/record.jl
@@ -511,9 +511,12 @@ end
 
 Get the segment sequence of `record`.
 """
-function sequence(record::Record)::BioSequences.LongDNASeq
+function sequence(record::Record)
     checkfilled(record)
     seqlen = seqlength(record)
+    if seqlen == 0
+        return nothing
+    end
     data = Vector{UInt64}(undef, cld(seqlen, 16))
     src::Ptr{UInt64} = pointer(record.data, seqname_length(record) + n_cigar_op(record, false) * 4 + 1)
     for i in 1:lastindex(data)
diff --git a/src/sam/record.jl b/src/sam/record.jl
index 2d94a12..dcddf42 100644
--- a/src/sam/record.jl
+++ b/src/sam/record.jl
@@ -206,9 +206,9 @@ Get the 1-based leftmost mapping position of `record`.
 function position(record::Record)::Int
     checkfilled(record)
     pos = unsafe_parse_decimal(Int, record.data, record.pos)
-    if pos == 0
-        missingerror(:position)
-    end
+    # if pos == 0
+    #     missingerror(:position)
+    # end
     return pos
 end
 
@@ -263,9 +263,9 @@ Get the position of the mate/next read of `record`.
 function nextposition(record::Record)::Int
     checkfilled(record)
     pos = unsafe_parse_decimal(Int, record.data, record.pnext)
-    if pos == 0
-        missingerror(:nextposition)
-    end
+    # if pos == 0
+    #     missingerror(:nextposition)
+    # end
     return pos
 end
 
@@ -299,7 +299,8 @@ Get the CIGAR string of `record`.
 function cigar(record::Record)::String
     checkfilled(record)
     if ismissing(record, record.cigar)
-        missingerror(:cigar)
+        # missingerror(:cigar)
+        return ""
     end
     return String(record.data[record.cigar])
 end
@@ -377,9 +378,9 @@ Get the template length of `record`.
 function templength(record::Record)::Int
     checkfilled(record)
     len = unsafe_parse_decimal(Int, record.data, record.tlen)
-    if len == 0
-        missingerror(:tlen)
-    end
+    # if len == 0
+    #     missingerror(:tlen)
+    # end
     return len
 end
 
@@ -392,10 +393,11 @@ end
 
 Get the segment sequence of `record`.
 """
-function sequence(record::Record)::BioSequences.LongDNASeq
+function sequence(record::Record)
     checkfilled(record)
     if ismissing(record, record.seq)
-        missingerror(:sequence)
+        # missingerror(:sequence)
+        return nothing
     end
     seqlen = length(record.seq)
     ret = BioSequences.LongDNASeq(seqlen)