From 73b87a66aeb59de08cad0db92d37334a6cfcf9f2 Mon Sep 17 00:00:00 2001
From: Erik Aronesty <erik@q32.com>
Date: Mon, 12 May 2014 11:25:28 -0400
Subject: [PATCH 1/2] add simple tests

---
 t/simple.t | 54 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 t/test1.fq | 12 ++++++++++++
 t/test2.fq | 12 ++++++++++++
 3 files changed, 78 insertions(+)
 create mode 100644 t/simple.t
 create mode 100644 t/test1.fq
 create mode 100644 t/test2.fq

diff --git a/t/simple.t b/t/simple.t
new file mode 100644
index 0000000..84a075a
--- /dev/null
+++ b/t/simple.t
@@ -0,0 +1,54 @@
+#!/usr/bin/perl
+
+use strict;
+use Test::More tests=>20;
+use File::Basename;
+use File::Spec;
+
+chdir(dirname(__FILE__));
+
+# set of very simple tests to check options and fastq i/o
+my $dsrc=File::Spec->catfile("..", "bin", "dsrc");
+
+for my $m (qw(m0 m1)) {
+for my $f (qw(test1 test2)) {
+
+    # remove prev out, if any
+    unlink "$f-$m.fq.out.dz", "$f-$m.fq.out";
+
+    # ****5 tests per loop*****
+
+
+    # standard test
+    sys("$dsrc c -m$m $f.fq $f-$m.fq.out.dz", "compress $m $f");
+    sys("$dsrc d $f-$m.fq.out.dz $f-$m.fq.out", "decompress $m $f");
+    same("$f.fq", "$f-$m.fq.out"); 
+
+    #  stream decompress
+    sys("$dsrc d -s $f-$m.fq.out.dz > $f-$m-s.fq.out", "decompress stream $m $f");
+    same("$f.fq", "$f-$m-s.fq.out"); 
+}
+}
+
+sub sys {
+    if (!ok(!system($_[0]), $_[1])) {
+        diag($_[0]);
+    }
+}
+
+sub slurp {
+    my ($f) = @_;
+    local $/= undef;
+    open S, $f;
+    my $r=<S>;
+    close S;
+    return $r;
+}
+
+sub same {
+    my ($f1, $f2) = @_;
+    my $r1=slurp($f1);
+    my $r2=slurp($f2);
+    ok($r1 && $r2 && ($r1 eq $r2), "$f1 = $f2");
+}
+
diff --git a/t/test1.fq b/t/test1.fq
new file mode 100644
index 0000000..12a15ca
--- /dev/null
+++ b/t/test1.fq
@@ -0,0 +1,12 @@
+@1 CLIP IS AGTCCCGTAC AT >=
+ATATGCTACGTTTGTGACCTAGTCCCGTAC
++
+hhhhhhhhhhhhhhhhhhhhhhhffgffaa
+@2 CLIP AGTCCCGTAC + AAAA's
+ATGTTCGTATATGAGCAGTCCCGTACAAAA
++
+hhbhhhhhhhhhhhhhhhhhhhhfffffaa
+@3 CLIP JUST AGTCC
+TATAGCCTCTAGCTTGACTCTAGCTAGTCC
++
+hhhhhhhhhhhhhhhhhhhhhhfffffaaa
diff --git a/t/test2.fq b/t/test2.fq
new file mode 100644
index 0000000..04ef3df
--- /dev/null
+++ b/t/test2.fq
@@ -0,0 +1,12 @@
+@1 CLIP IS AGTCCCGTAC AT END
+ATATGCTACGTTTGTGACCTAGTCCCGTAC
++
+hhhhhhhhhhhhhhhhhhhhhhhffgffaa
+@2 CLIP AGTCCCGTAC + AAAAs
+ATGTTCGTATATGAGCAGTCCCGTACAAAA
++
+hhbhhhhhhhhhhhhhhhhhhhhfffffhh
+@3 CLIP JUST AGTCC
+TATAGCCTCTAGCTTGACTCTAGCTAGTCC
++
+hhhhhhhhhhhhhhhhhhhhhhfffffhhh

From 6c99a6c4773c8d202961d0c4b6b1324543d01435 Mon Sep 17 00:00:00 2001
From: Erik Aronesty <erik@q32.com>
Date: Wed, 13 Aug 2014 12:05:34 -0400
Subject: [PATCH 2/2] t2

---
 t/test2.fq | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/t/test2.fq b/t/test2.fq
index 04ef3df..fce79c8 100644
--- a/t/test2.fq
+++ b/t/test2.fq
@@ -1,12 +1,12 @@
-@1 CLIP IS AGTCCCGTAC AT END
+@1 a b c; ; ;=<
 ATATGCTACGTTTGTGACCTAGTCCCGTAC
 +
 hhhhhhhhhhhhhhhhhhhhhhhffgffaa
-@2 CLIP AGTCCCGTAC + AAAAs
+@2 a b c 
 ATGTTCGTATATGAGCAGTCCCGTACAAAA
 +
 hhbhhhhhhhhhhhhhhhhhhhhfffffhh
-@3 CLIP JUST AGTCC
+@3 a b c
 TATAGCCTCTAGCTTGACTCTAGCTAGTCC
 +
 hhhhhhhhhhhhhhhhhhhhhhfffffhhh