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sfchensfchen
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Merge pull request #11 from chinwobble/update-tests
enable tests for stats and fastqreader
2 parents a044607 + d4ce0bc commit 2fb8ecc

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6 files changed

+135
-17
lines changed

6 files changed

+135
-17
lines changed

‎CMakeLists.txt‎

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@@ -73,6 +73,7 @@ set(
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test/globals.cpp
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test/polyx_test.cpp
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test/sequence_test.cpp
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test/stats_test.cpp
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)
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include_directories(
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# intel mac install location
@@ -117,7 +118,12 @@ target_link_libraries(
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# tests target
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enable_testing()
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find_package(GTest CONFIG REQUIRED)
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configure_file(test/config.h.in ${CMAKE_BINARY_DIR}/include/config.h)
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add_executable(fastplong_tests ${FASTPLONG_TEST_SOURCES})
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target_include_directories(
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fastplong_tests
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PRIVATE ${CMAKE_BINARY_DIR}/include
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)
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target_link_libraries(
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fastplong_tests PRIVATE
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${FASTPLONG_LIBS}

‎test/config.h.in‎

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// this file is necessary to help resolve the correct path when loading test data files.
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// When tests using the IDE and CLI the working directory can be different.
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// This substitute builds the absolute path to eliminate the need to depend on the working directory.
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#pragma once
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#define FP_TESTDATA_R1 "${CMAKE_SOURCE_DIR}/testdata/R1.fq"
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#define FP_TESTDATA_R2 "${CMAKE_SOURCE_DIR}/testdata/R2.fq"

‎test/fastqreader_test.cpp‎

Lines changed: 27 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -1,22 +1,32 @@
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#include <gtest/gtest.h>
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#include "../src/fastqreader.h"
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4-
TEST(fastqreader, test) {
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/*FastqReader reader1("testdata/R1.fq");
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FastqReader reader2("testdata/R1.fq");
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Read* r1 = NULL;
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Read* r2 = NULL;
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int i=0;
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while(true){
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i++;
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r1=reader1.read();
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r2=reader2.read();
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if(r1 == NULL || r2==NULL)
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#include "config.h"
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#include <vector>
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TEST(fastqreader, test)
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{
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FastqReader reader1(FP_TESTDATA_R1);
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Read *r1 = NULL;
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std::vector<Read*> v;
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while (true)
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{
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r1 = reader1.read();
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if (r1 == nullptr) {
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break;
16-
r1->print();
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r2->print();
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delete r1;
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delete r2;
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}*/
21-
}
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}
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v.push_back(r1);
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}
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EXPECT_EQ(v.size(), 9);
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EXPECT_EQ(*v[0]->mName, "@AS500713:64:HFKJJBGXY:1:11101:1675:1101 1:A:0:TATAGCCT+GACCCCCA");
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EXPECT_EQ(*v[0]->mSeq, "");
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EXPECT_EQ(*v[0]->mStrand, "+");
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EXPECT_EQ(*v[0]->mQuality, "");
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EXPECT_EQ(*v[1]->mName, "@AS500713:64:HFKJJBGXY:1:11101:17113:1101 1:A:0:TATAGCCT+GTTTCTTA");
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EXPECT_EQ(*v[1]->mSeq, "TACAAAATGCACATCGCTGAAAGGGGTAAAGGAGAGAAATCGCTTTATAAAACCTTGAAAAGGAATATTCAAATATAAGCTGGGAAGGTATAAAAAACTCTGTACATCACAAGTAAACAAATGGAACCTGCAAAATATTAAACAAAGGATT");
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EXPECT_EQ(*v[1]->mStrand, "+");
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EXPECT_EQ(*v[1]->mQuality, "AAAAAEEEEE6EEAAAEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEECFE####EEEE6EE<AAEEEAEEEEEEEEEEEEAEEEEEEEA<E/AAEEEAEEEEE/EEEEAAEEE");
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}

‎test/stats_test.cpp‎

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#include <gtest/gtest.h>
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#include "../src/stats.h"
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#include "../src/evaluator.h"
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#include <algorithm>
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TEST(StatsTests, summarise) {
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Read* left = new Read(
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new string("@NS500713:64:HFKJJBGXY:1:11101:20469:1097 1:N:0:TATAGCCT+GGTCCCGA"),
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new string("TTTTTTCTCTTGGACTCTAACACTGTTTTTTCTTATGAAAACACAGGAGTGATGACTAGTTGAGTGCATTCTTATGAGACTCATAGTCATTCTATGATGTAG"),
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new string("+"),
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new string("AAAAA6EEEEEEEEEEEEEEEEE#EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE"));
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Options* options = new Options();
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Stats stats(options);
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stats.statRead(left);
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stats.summarize();
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EXPECT_EQ(stats.getCycles(), 102);
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EXPECT_EQ(stats.getBases(), 102);
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EXPECT_EQ(stats.getReads(), 1);
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EXPECT_EQ(stats.getQ20(), 101);
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EXPECT_EQ(stats.getQ30(), 100);
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EXPECT_EQ(stats.getGCNumber(), 35);
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}

‎testdata/R1.fq‎

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@AS500713:64:HFKJJBGXY:1:11101:1675:1101 1:A:0:TATAGCCT+GACCCCCA
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+
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@AS500713:64:HFKJJBGXY:1:11101:17113:1101 1:A:0:TATAGCCT+GTTTCTTA
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TACAAAATGCACATCGCTGAAAGGGGTAAAGGAGAGAAATCGCTTTATAAAACCTTGAAAAGGAATATTCAAATATAAGCTGGGAAGGTATAAAAAACTCTGTACATCACAAGTAAACAAATGGAACCTGCAAAATATTAAACAAAGGATT
7+
+
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AAAAAEEEEE6EEAAAEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEECFE####EEEE6EE<AAEEEAEEEEEEEEEEEEAEEEEEEEA<E/AAEEEAEEEEE/EEEEAAEEE
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@AS500713:64:HFKJJBGXY:1:11101:1675:1101 1:A:0:TATAGCCT+GACCCCCA
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TAGGAGGCTTGGAGTACCAATAATAAAGTGAGCCCACCTTCCTGGTACCCAGACATTTCAGGAGGTCGGGAAATTTTTAAACCCAGGCAGCTTCCTGGCAGTGACATTTGGAGCATCAAAGTGGTAAATAAAATTTCATTTACATTAATAT
11+
+
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6AAAAAEEEEE/E/EA/E/AEA6EE//AEE66/AAE//EEE/E//E/AA/EEE/A/AEE/EEA//EEEEEEEE6EEAAA/E###6E/6//6<EAAEEE/EEEA/EA/EEEEEE/<<EEEE//A/EE<AEEEEE/</AA</E<AAAE/E<E/
13+
@AS500713:64:HFKJJBGXY:1:11101:17113:1101 1:A:0:TATAGCCT+GTTTCTTA
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TACAAAATGCACATCGCTGAAAGGGGTAAAGGAGAGAAATCGCTTTATAAAACCTTGAAAAGGAATATTCAAATATAAGCTGGGAAGGTATAAAAAACTCTGTACATCACAAGTAAACAAATGGAACCTGCAAAATATTAAACAAAGGATT
15+
+
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AAAAAEEEEE6EEAAAEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEEEEE/EEEEEEE6EE<AAEEEAEEEEEEEEEEEEAEEEEEEEA<E/AAEEEAEEEEE/EEEEAAEEE
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@AS500713:64:HFKJJBGXY:1:11101:1675:1101 1:A:0:TATAGCCT+GACCCCCA
18+
TAGGAGGCTTGGAGTACCAATAATAAAGTGAGCCCACCTTCCTGGTACCCAGACATTTCAGGAGGTCGGGAAATTTTTAAACCCAGGCAGCTTCCTGGCAGTGACATTTGGAGCATCAAAGTGGTAAATAAAATTTCATTTACATTAATAT
19+
+
20+
6AAAAAEEEEE/E/EA/E/AEA6EE//AEE66/AAE//EEE/E//E/AA/EEE/A/AEE/EEA//EEEEEEEE6EEAAA/E/A/6E/6//6<EAAEEE/EEEA/EA/EEEEEE/<<EEEE//A/EE<AEEEEE/</AA</E<AAAE/E<E/
21+
@AS500713:64:HFKJJBGXY:1:11101:17113:1101 1:A:0:TATAGCCT+GTTTCTTA
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TACAAAATGCACATCGCTGAAAGGGGTAAAGGAGAGAAATCGCTTTATAAAACCTTGAAAAGGAATATTCAAATATAAGCTGGGAAGGTATAAAAAACTCTGTACATCACAAGTAAACAAATGGAACCTGCAAAATATTAAACAAAGGATT
23+
+
24+
AAAAAEEEEE6EEAAAEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEEEEE/EEEEEEE6EE<AAEEEAEEEEEEEEEEEEAEEEEEEEA<E/AAEEEAEEEEE/EEEEAAEEE
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@AS500713:64:HFKJJBGXY:1:11101:1675:1101 1:A:0:TATAGCCT+GACCCCCA
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TAGGAGGCTTGGAGTACCAATAATAAAGTGAGCCCACCTTCCTGGTACCCAGACATTTCAGGAGGTCGGGAAATTTTTAAACCCAGGCAGCTTCCTGGCAGTGACATTTGGAGCATCAAAGTGGTAAATAAAATTTCATTTACATTAATAT
27+
+
28+
6AAAAAEEEEE/E/EA/E/AEA6EE//AEE66/AAE//EEE/E//E/AA/EEE/A/AEE/EEA//EEEEEEEE6EEAAA/E/A/6E/6//6<EAAEEE/EEEA/EA/EEEEEE/<<EEEE//A/EE<AEEEEE/</AA</E<AAAE/E<E/
29+
@AS500713:64:HFKJJBGXY:1:11101:17113:1101 1:A:0:TATAGCCT+GTTTCTTA
30+
TACAAAATGCACATCGCTGAAAGGGGTAAAGGAGAGAAATCGCTTTATAAAACCTTGAAAAGGAATATTCAAATATAAGCTGGGAAGGTATAAAAAACTCTGTACATCACAAGTAAACAAATGGAACCTGCAAAATATTAAACAAAGGATT
31+
+
32+
AAAAAEEEEE6EEAAAEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEEEEE/EEEEEEE6EE<AAEEEAEEEEEEEEEEEEAEEEEEEEA<E/AAEEEAEEEEE/EEEEAAEEE
33+
@AS500713:64:HFKJJBGXY:1:11101:17113:1101 1:A:0:TATAGCCT+GTTTCTTA
34+
CCCCCCCCCCACATCGCTGAAAGGGGTAAAGGAGAGAAATCGCTTTATAAAACCTTGAAAAGGAATATTCAAATATAAGCTGGGAAGGTATAAAAAACTCTGTACATCACAAGTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
35+
+
36+
AAAAAEEEEE6EEAAAEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEEEEE/EEEEEEE6EE<AAEEEAEEEEEEEEEEEEAEEEEEEEA<E/AAEEEAEEEEE/EEEEAAEEE

‎testdata/R2.fq‎

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@AS500713:64:HFKJJBGXY:1:11101:1675:1101 2:A:0:TATAGCCT+GACCCCCA
2+
TAGGGCAAAACAAATAAGACAAAAAAAAAAAATGAATGAAAATGCAATTTTATTTACCACTTTGATGCTCAAAATGGCACTGCCAGGAAGCTGCCTGGGTTTAAAAATTTCCCGACCTCCTGAAATGTCTGGGGACCAGGAAGGTGGGCTC
3+
+
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AAAAA/EEEA/EEEE#AEA<####E######EE/A#E/##EEEE/E<<EEEE6EEAA/EAE<AEEEAAEE/EEEA/</EEEE6//</A///A6E<6E/AEEEEEEEEEEA<<6//<A</<<AAEEE/</A///<E<<A//EEAE</E/AA6
5+
@AS500713:64:HFKJJBGXY:1:11101:17113:1101 2:A:0:TATAGCCT+GTTTCTTA
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CTAAATTGAGTAATGAAGATAAAATAAAAAATAACAAAAACTTTGTTTAATATTTTGCAGGTTCCATTTGTTTACTTGTGATGTACAGAGTTTTTTATACCTTCCCAGCTTATATTTGAATATTCCTTTTCAAGGTTTTATAAAGCGATTT
7+
+
8+
AAAAAEEEEEEEEEE#EEEE####E######E#EE#E###EEEEEEE/AEEEEEEEE/EEEE<EAEEEEEEEEE/EEEEEEEEEE<EEEEAEEEEEEEE<6EEA6<EE6EEEEEEEEEEAEAEEE/A<AE<AEEAEEEEEEEEE/</AAAA
9+
@AS500713:64:HFKJJBGXY:1:11101:1675:1101 2:A:0:TATAGCCT+GACCCCCA
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TAGGGCAAAACAAATAAGACAAAAAAAAAAAATGAATGAAAATGCAATTTTATTTACCACTTTGATGCTCAAAATGGCACTGCCAGGAAGCTGCCTGGGTTTAAAAATTTCCCGACCTCCTGAAATGTCTGGGGACCAGGAAGGTGGGCTC
11+
+
12+
AAAAA/EEEA/EEEE#AEA<####E######EE/A#E/##EEEE/E<<EEEE6EEAA/EAE<AEEEAAEE/EEEA/</EEEE6//</A///A6E<6E/AEEEEEEEEEEA<<6//<A</<<AAEEE/</A///<E<<A//EEAE</E/AA6
13+
@AS500713:64:HFKJJBGXY:1:11101:17113:1101 2:A:0:TATAGCCT+GTTTCTTA
14+
CTAAATTGAGTAATGAAGATAAAATAAAAAATAACAAAAACTTTGTTTAATATTTTGCAGGTTCCATTTGTTTACTTGTGATGTACAGAGTTTTTTATACCTTCCCAGCTTATATTTGAATATTCCTTTTCAAGGTTTTATAAAGCGATTT
15+
+
16+
AAAAAEEEEEEEEEE#EEEE####E######E#EE#E###EEEEEEE/AEEEEEEEE/EEEE<EAEEEEEEEEE/EEEEEEEEEE<EEEEAEEEEEEEE<6EEA6<EE6EEEEEEEEEEAEAEEE/A<AE<AEEAEEEEEEEEE/</AAAA
17+
@AS500713:64:HFKJJBGXY:1:11101:1675:1101 2:A:0:TATAGCCT+GACCCCCA
18+
TAGGGCAAAACAAATAAGACAAAAAAAAAAAATGAATGAAAATGCAATTTTATTTACCACTTTGATGCTCAAAATGGCACTGCCAGGAAGCTGCCTGGGTTTAAAAATTTCCCGACCTCCTGAAATGTCTGGGGACCAGGAAGGTGGGCTC
19+
+
20+
AAAAA/EEEA/EEEE#AEA<####E######EE/A#E/##EEEE/E<<EEEE6EEAA/EAE<AEEEAAEE/EEEA/</EEEE6//</A///A6E<6E/AEEEEEEEEEEA<<6//<A</<<AAEEE/</A///<E<<A//EEAE</E/AA6
21+
@AS500713:64:HFKJJBGXY:1:11101:17113:1101 2:A:0:TATAGCCT+GTTTCTTA
22+
CTAAATTGAGTAATGAAGATAAAATAAAAAATAACAAAAACTTTGTTTAATATTTTGCAGGTTCCATTTGTTTACTTGTGATGTACAGAGTTTTTTATACCTTCCCAGCTTATATTTGAATATTCCTTTTCAAGGTTTTATAAAGCGATTT
23+
+
24+
AAAAAEEEEEEEEEE#EEEE####E######E#EE#E###EEEEEEE/AEEEEEEEE/EEEE<EAEEEEEEEEE/EEEEEEEEEE<EEEEAEEEEEEEE<6EEA6<EE6EEEEEEEEEEAEAEEE/A<AE<AEEAEEEEEEEEE/</AAAA
25+
@AS500713:64:HFKJJBGXY:1:11101:1675:1101 2:A:0:TATAGCCT+GACCCCCA
26+
TAGGGCAAAACAAATAAGACAAAAAAAAAAAATGAATGAAAATGCAATTTTATTTACCACTTTGATGCTCAAAATGGCACTGCCAGGAAGCTGCCTGGGTTTAAAAATTTCCCGACCTCCTGAAATGTCTGGGGACCAGGAAGGTGGGCTC
27+
+
28+
AAAAA/EEEA/EEEE#AEA<####E######EE/A#E/##EEEE/E<<EEEE6EEAA/EAE<AEEEAAEE/EEEA/</EEEE6//</A///A6E<6E/AEEEEEEEEEEA<<6//<A</<<AAEEE/</A///<E<<A//EEAE</E/AA6
29+
@AS500713:64:HFKJJBGXY:1:11101:17113:1101 2:A:0:TATAGCCT+GTTTCTTA
30+
CTAAATTGAGTAATGAAGATAAAATAAAAAATAACAAAAACTTTGTTTAATATTTTGCAGGTTCCATTTGTTTACTTGTGATGTACAGAGTTTTTTATACCTTCCCAGCTTATATTTGAATATTCCTTTTCAAGGTTTTATAAAGCGATTT
31+
+
32+
AAAAAEEEEEEEEEE#EEEE####E######E#EE#E###EEEEEEE/AEEEEEEEE/EEEE<EAEEEEEEEEE/EEEEEEEEEE<EEEEAEEEEEEEE<6EEA6<EE6EEEEEEEEEEAEAEEE/A<AE<AEEAEEEEEEEEE/</AAAA
33+
@AS500713:64:HFKJJBGXY:1:11101:17113:1101 1:A:0:TATAGCCT+GTTTCTTA
34+
TACAAAATGCACATCGCTGAAAGGGGTAAAGGAGAGAAATCGCTTTATAAAACCTTGAAAAGGAATATTCAAATATAAGCTGGGAAGGTATAAAAAACTCTGTACATCACAAGTAAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
35+
+
36+
AAAAAEEEEE6EEAAAEEEEE6EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEEEEEEEEEEEEE/EEEEEEE6EE<AAEEEAEEEEEEEEEEEEAEEEEEEEA<E/AAEEEAEEEEE/EEEEAAEEE

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