From 2df146b8fc4578e9631def931bb6441575603b13 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ciar=C3=A1n=20O=27Mara?= <Ciaran.OMara@utas.edu.au>
Date: Sun, 2 Feb 2020 22:44:55 +1100
Subject: [PATCH] Use FormatSpecimens

---
 Project.toml     |  4 ++--
 test/runtests.jl | 18 +++++++++---------
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/Project.toml b/Project.toml
index 2f31d67..18608d4 100644
--- a/Project.toml
+++ b/Project.toml
@@ -26,8 +26,8 @@ Indexes = "0.1"
 julia = "1.1"
 
 [extras]
+FormatSpecimens = "3372ea36-2a1a-11e9-3eb7-996970b6ffbd"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 
 [targets]
-test = ["Test", "YAML"]
+test = ["FormatSpecimens", "Test"]
diff --git a/test/runtests.jl b/test/runtests.jl
index 7594e1c..ffb2669 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -2,11 +2,11 @@ using Test
 using GenomicFeatures
 using XAM
 import BioAlignments: Alignment, AlignmentAnchor, OP_START, OP_MATCH, OP_DELETE
+using FormatSpecimens
 import BGZFStreams: BGZFStream
 import BioCore.Exceptions: MissingFieldException
-import BioCore.Testing.get_bio_fmt_specimens
 import BioSequences: @dna_str, @aa_str
-import YAML
+
 
 import BioCore:
     header,
@@ -32,7 +32,7 @@ function randrange(range)
 end
 
 @testset "SAM" begin
-    samdir = joinpath(get_bio_fmt_specimens("master", false, true), "SAM")
+    samdir = path_of_format("SAM")
 
     @testset "MetaInfo" begin
         metainfo = SAM.MetaInfo()
@@ -172,8 +172,8 @@ end
             end
             return true
         end
-        for specimen in YAML.load_file(joinpath(samdir, "index.yml"))
-            filepath = joinpath(samdir, specimen["filename"])
+        for specimen in list_valid_specimens("SAM")
+            filepath = joinpath(samdir, filename(specimen))
             mktemp() do path, io
                 # copy
                 reader = open(SAM.Reader, filepath)
@@ -192,7 +192,7 @@ end
 end
 
 @testset "BAM" begin
-    bamdir = joinpath(get_bio_fmt_specimens("master", false), "BAM")
+    bamdir = path_of_format("BAM")
 
     @testset "AuxData" begin
         auxdata = BAM.AuxData(UInt8[])
@@ -370,11 +370,11 @@ end
     end
 
     @testset "Round trip" begin
-        for specimen in YAML.load_file(joinpath(bamdir, "index.yml"))
-            filepath = joinpath(bamdir, specimen["filename"])
+        for specimen in list_valid_specimens("BAM")
+            filepath = joinpath(bamdir, filename(specimen))
             mktemp() do path, _
                 # copy
-                if occursin("bai", get(specimen, "tags", ""))
+                if hastags(specimen) && in("bai", tags(specimen))
                     reader = open(BAM.Reader, filepath, index=filepath * ".bai")
                 else
                     reader = open(BAM.Reader, filepath)