From 8c94a226b9eb2267195b364e056913ada69a0e5f Mon Sep 17 00:00:00 2001
From: Mikael Salson <mikael.salson@univ-lille1.fr>
Date: Tue, 10 Jul 2018 19:55:24 +0200
Subject: [PATCH] 
 germline/tests/should-get-tests/upstream-order-IGHD.should-get: Check IGHD
 order

Make sure that IGHD and IGHD+up orders are identical and that the
IGHD+up looks ok.

See #3148
---
 .../tests/should-get-tests/upstream-order-IGHD.should-get | 8 ++++++++
 1 file changed, 8 insertions(+)
 create mode 100644 germline/tests/should-get-tests/upstream-order-IGHD.should-get

diff --git a/germline/tests/should-get-tests/upstream-order-IGHD.should-get b/germline/tests/should-get-tests/upstream-order-IGHD.should-get
new file mode 100644
index 000000000..b0d74b4e5
--- /dev/null
+++ b/germline/tests/should-get-tests/upstream-order-IGHD.should-get
@@ -0,0 +1,8 @@
+cd $VIDJIL_DIR/germline
+awk -F '|' '$0 ~ /^>/ {print $2}' homo-sapiens/IGHD.fa > tmp_ighdnames && \
+awk -F '|' '$0 ~ /^>/ {print $2}' homo-sapiens/IGHD+up.fa > tmp_ighdupnames && \
+cat tmp_ighdupnames && \
+diff -q tmp_ighdnames tmp_ighdupnames && rm -f tmp_ighdupnames tmp_ighdnames
+
+$ Some genes in correct relative order
+l1: IGHD1-1.01.*IGHD1-14.01.*IGHD1-20.01.*IGHD1-26.01.*IGHD1-7.01.*IGHD1/OR15-1a.*IGHD1/OR15-1b.*IGHD2-15
-- 
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