[med-svn] [Git][med-team/maqview][master] 5 commits: Install test and reference data

Pranav Ballaney gitlab at salsa.debian.org
Wed Jul 1 16:10:56 BST 2020 


Pranav Ballaney pushed to branch master at Debian Med / maqview


Commits:
2d2cb28a by Pranav Ballaney at 2020-07-01T20:26:07+05:30
Install test and reference data

- - - - -
cd0ca185 by Pranav Ballaney at 2020-07-01T20:29:07+05:30
Add autopkgtests

- - - - -
40c11e16 by Pranav Ballaney at 2020-07-01T20:30:00+05:30
Install docs

- - - - -
0c1b695d by Pranav Ballaney at 2020-07-01T20:38:58+05:30
Include reference file binaries

- - - - -
6ae8c65c by Pranav Ballaney at 2020-07-01T20:40:01+05:30
Add Pranav Ballaney to Uploaders

- - - - -


25 changed files:

- + debian/README.test
- debian/changelog
- debian/control
- debian/docs
- + debian/examples
- + debian/source/include-binaries
- + debian/tests/README.test_data
- + debian/tests/control
- + debian/tests/data/test.fa
- + debian/tests/data/test.fastq
- + debian/tests/ref/cns.cns.summary
- + debian/tests/ref/cns.cns.zr
- + debian/tests/ref/maqindex1/part1.map.vm
- + debian/tests/ref/maqindex1/part1.map.zr
- + debian/tests/ref/maqindex2/cns.cns.summary
- + debian/tests/ref/maqindex2/cns.cns.zr
- + debian/tests/ref/maqindex2/part1.map.vm
- + debian/tests/ref/maqindex2/part1.map.zr
- + debian/tests/ref/maqindex3/cns.cns.summary
- + debian/tests/ref/maqindex3/cns.cns.zr
- + debian/tests/ref/part1.map.vm
- + debian/tests/ref/part1.map.zr
- + debian/tests/ref/test.fa.gz.zr
- + debian/tests/ref/zrio.use.out
- + debian/tests/run-unit-test


Changes:

=====================================
debian/README.test
=====================================
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+    sh run-unit-test
+
+in order to confirm its integrity.


=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+maqview (0.2.5-10) UNRELEASED; urgency=medium
+
+  * Install test and reference data
+  * Add autopkgtests
+  * Install docs
+  * Include reference file binaries
+  * Add Pranav Ballaney to Uploaders
+
+ -- Pranav Ballaney <ballaneypranav at gmail.com>  Wed, 01 Jul 2020 20:29:11 +0530
+
 maqview (0.2.5-9) unstable; urgency=medium
 
   * debhelper 11


=====================================
debian/control
=====================================
@@ -1,7 +1,8 @@
 Source: maqview
 Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille at debian.org>,
-           Charles Plessy <plessy at debian.org>
+           Charles Plessy <plessy at debian.org>,
+           Pranav Ballaney <ballaneypranav at gmail.com>
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 11~),


=====================================
debian/docs
=====================================
@@ -1,2 +1,5 @@
 NEWS
 README
+debian/README*
+debian/tests/README*
+debian/tests/run-unit-test
\ No newline at end of file


=====================================
debian/examples
=====================================
@@ -0,0 +1,2 @@
+debian/tests/data
+debian/tests/ref
\ No newline at end of file


=====================================
debian/source/include-binaries
=====================================
@@ -0,0 +1,10 @@
+debian/tests/ref/part1.map.zr
+debian/tests/ref/part1.map.vm
+debian/tests/ref/cns.cns.zr
+debian/tests/ref/test.fa.gz.zr
+debian/tests/ref/maqindex3/cns.cns.zr
+debian/tests/ref/maqindex1/part1.map.zr
+debian/tests/ref/maqindex1/part1.map.vm
+debian/tests/ref/maqindex2/part1.map.zr
+debian/tests/ref/maqindex2/part1.map.vm
+debian/tests/ref/maqindex2/cns.cns.zr
\ No newline at end of file


=====================================
debian/tests/README.test_data
=====================================
@@ -0,0 +1,5 @@
+Files in debian/tests/data were obtained from the test data for the Debian packaging for maq.
+(https://salsa.debian.org/med-team/maq/-/tree/master/debian/maq.tests)
+
+Files in debian/tets/ref were generated by processing the data files as described in
+debian/tests/run-unit-test and are added here only for reference.
\ No newline at end of file


=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, maq
+Restrictions: allow-stderr


=====================================
debian/tests/data/test.fa
=====================================
@@ -0,0 +1,11 @@
+>gnl|MYDB|1 this is sequence 1
+GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG
+TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA
+GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT
+GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG
+GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT
+TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG
+CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT
+TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT
+CACAGACAGCCTGAGACAGTTCTTACGGAAACACCCCAGGACACAATTGAATTAAACAGATTGAATTTAGAATCTTCCAA
+


=====================================
debian/tests/data/test.fastq
=====================================
@@ -0,0 +1,501 @@
+ at HWI-EAS_4_PE-FC20GCB:2:1:492:573/2
+ACAGCAAAATTGTGATTGAGGATGAAGAACTGCTGT
++
+AA7AAA3+AAAAAA.AAA.;7;AA;;;;*;<1;<<<
+ at HWI-EAS_4_PE-FC20GCB:2:1:353:708/2
+AATACTGATTGTTAGTTAATTTATATTAAGTAGCGC
++
+AAAAAAAAAAAA3AAAAAAAAAAAAAAAA2>?(<6:
+ at HWI-EAS_4_PE-FC20GCB:2:1:188:749/2
+ATTTATCGTATAGCCCCATTATTTATTCTCCAGCCA
++
+AAAAAAAAAAAAAAAAA?AA>AAA>AA???>//<9+
+ at HWI-EAS_4_PE-FC20GCB:2:1:289:559/2
+TGTTAACAAACAAGGAGAAAACAGTATGAAACACGG
++
+AAAAAAAAAAAAAAA?AAAAAAAAAAAAAA<><><<
+ at HWI-EAS_4_PE-FC20GCB:2:1:292:704/2
+TATCCACACCTGTGCCAGGAACTTCCTGAGCAACAG
++
+AAAAAAAAAAAA?AAAAAAAAAAAAAAAA=?>6>?0
+ at HWI-EAS_4_PE-FC20GCB:2:1:387:804/2
+GATGAGGATGGGAGTTGTTTTATTGCTTTAGTTTTA
++
+AAAAAAA*AAAA.AAAAAAAAAAA7AAAA;.<6&<:
+ at HWI-EAS_4_PE-FC20GCB:2:1:386:461/2
+CGTAACTTCCTGGACCGACGTACTGCCAGAATTCGG
++
+AAAAAAAAAAAAAAAA?AAAAAAAAAA<AA9>/>66
+ at HWI-EAS_4_PE-FC20GCB:2:1:143:673/2
+CATGTCACATTTTTTCACGCTATTTGTTGGAGAACA
++
+AAAAAA5AAAAA?5;A?A5AA;AAA.AA3+;.-;?;
+ at HWI-EAS_4_PE-FC20GCB:2:1:199:702/2
+GTGGGCAGCAACTTCAGCGTGAAATCGCCGAACGTG
++
+A<AAAAAAAAAAAAAA<AA<AA<9A>AAAA><?98<
+ at HWI-EAS_4_PE-FC20GCB:2:1:416:494/2
+AAATTCAAAAAGAAACTTTTGATAAAGTAATGACAT
++
+AAAAAAAAA<AAAAAAAA%AA<AAA>5><>?<??>9
+ at HWI-EAS_4_PE-FC20GCB:2:1:186:430/2
+TTATCTTTATGTGAATCTCATTTTTTATAATGATGT
++
+A5AA?AAA?A;A?AA?5A??AAAAA>8AA+?.??.;
+ at HWI-EAS_4_PE-FC20GCB:2:1:259:697/2
+TTATTAACTTTATCCGCCAGCAAGCGGCAAATCTCT
++
+AAAAAAAAAAAAAAAAAAAAAAAAAA=AAA0>?>??
+ at HWI-EAS_4_PE-FC20GCB:2:1:304:517/2
+TAGATTAAATACGATAAGTTAAGCATCATCTCTCAT
++
+AAAAAA9.AA9A=3A=93=A3=3A=AA363<<;<;2
+ at HWI-EAS_4_PE-FC20GCB:2:1:257:905/2
+TAAATGATCGCTCTGTTTGCAATATTGTTTTTAATG
++
+AAAAAAAAAAAAAAAAAAAAAAAAAA=AAA??%0?+
+ at HWI-EAS_4_PE-FC20GCB:2:1:244:675/2
+TTTTTCAAACTGGGTTTTGATCTCCAGTTTATTACG
++
+AAAAAAAAAAAAAAAAAA;AAAAA9=7AAA:??660
+ at HWI-EAS_4_PE-FC20GCB:2:1:378:409/2
+TTTTTAGAGTTTCTCGATATCAATTGCCTGAATAGC
++
+AAAAAAAAAAAAAAA;AAAAAAAAA?<AA6<6699/
+ at HWI-EAS_4_PE-FC20GCB:2:1:288:762/2
+AAATCATTTAACGCATCTTCCAGACAGTATGATTCA
++
+AAAAAAAAAA*AAA7AAA;AA777A6;A*A6)6<<.
+ at HWI-EAS_4_PE-FC20GCB:2:1:258:492/2
+CGTAAAATATTGCGCCAGGGCTGCAATGACAAATAT
++
+AAAAAAAAAAAAAAAAAAA?AAAAA*A??<9<>?<?
+ at HWI-EAS_4_PE-FC20GCB:2:1:541:553/2
+TCCCTGGGTCACCTTGATGACTTCCACGTTGTTTTT
++
+7+.*3337.+7;.+3733A+&*&*-66;&A1<1.<.
+ at HWI-EAS_4_PE-FC20GCB:2:1:301:548/2
+CAGGTGAGAGATATTTTCTTATTTGTGTGGTGAATG
++
+=A=A.A9=3=9=A9==A=AA9AAA,;.;.&<.6-<.
+ at HWI-EAS_4_PE-FC20GCB:2:1:397:790/2
+ATCCATCGTTTTAACAATGGGCTGCATACTCAGAAC
++
+AAAAAAAAAAAA++AAAA??>AA>A<AA*?<<%<<6
+ at HWI-EAS_4_PE-FC20GCB:2:1:529:669/2
+GACGCCACCACACTCCACAGCGCGTTGATCTGTTCC
++
+93339A9.9AA9.+9=3=3&99A93A336A62%2.;
+ at HWI-EAS_4_PE-FC20GCB:2:1:287:685/2
+TGATCGGTCAACTCCAGAATCTCATTGTCAGGCATA
++
+AAAAAAAAAAAAAA?AA?AAAAA?AAAA7=666>>:
+ at HWI-EAS_4_PE-FC20GCB:2:1:351:597/2
+TGATGACAAAAGTTACACCGTCAGACGTGCTACGCC
++
+AAAAAAAAAAAA?3AAAAAAAAAAAAAA&0>>>6<:
+ at HWI-EAS_4_PE-FC20GCB:2:1:385:762/2
+CTGGATCATAAATTAGCGGCACAACTCGGTATCGGG
++
+AAAAAAAAA<A<A<*AAA<AAAAAAAA<>>9??599
+ at HWI-EAS_4_PE-FC20GCB:2:1:208:643/2
+CTTTACGCATTTTATCGACGTAATAGGTTGAAGGAA
++
+AAAAAAAAAAAAAAAA?AAAAAAA?AAAAA<?26>6
+ at HWI-EAS_4_PE-FC20GCB:2:1:184:411/2
+CGTTGCAGCTCAGCTCTACTGGCAGGGTGAAGTCAT
++
+AAAAAA.AAAAAAAAAA=AA=3AA=A;+6.62*2-<
+ at HWI-EAS_4_PE-FC20GCB:2:1:403:699/2
+CCTAAGCCAACGACACCGACATGAAACTCAGATCCC
++
+AAAAAAAAAAAAA1?AAA+AAAAAA?A?A<9<4?>?
+ at HWI-EAS_4_PE-FC20GCB:2:1:340:602/2
+TAGTCGACAATAAAGGTCAGCGTTATACCGCCGATG
++
+AAAAAAAAAA<AAAAAAAAAAAAAAAAA5<?99?99
+ at HWI-EAS_4_PE-FC20GCB:2:1:330:641/2
+TGAAAAAGGCATTGGGATTTATGCCGTATTCCTGTA
++
+AAAAAAAAAA<AAAAA<AAAAAAAA<AAAA9>?>%<
+ at HWI-EAS_4_PE-FC20GCB:2:1:221:646/2
+TTTTTCGTGAGTATTCTTAGCGCCAGTTTGGTTTGG
++
+AAAAAA9A.A3A9AA=AA339.9=3.AAAA&<.<+*
+ at HWI-EAS_4_PE-FC20GCB:2:1:151:345/2
+CTATTTATTGGCCGCAGTTTTTCCCGTAGCGAGGCG
++
+AAAAAAAAAAAAAA?A?AAAAA1A+AA?+<//69/<
+ at HWI-EAS_4_PE-FC20GCB:2:1:166:739/2
+TATATCATCGCACGACCGCAGTCGGGTTATTACGTT
++
+AAAAAAAAAAAAAAAAAAA:AAAA?A?A=A?:>6?<
+ at HWI-EAS_4_PE-FC20GCB:2:1:398:570/2
+AGACTGTTGATAAAACGTAAAAAGGAATGCTCTGTT
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAA??????<
+ at HWI-EAS_4_PE-FC20GCB:2:1:298:584/2
+TAATAGCACAATTTTCATACTATTTTTTGGCATTCT
++
+AAAAAAAAAAAAAAAAAAAAA?AAAAAA=&>:??:?
+ at HWI-EAS_4_PE-FC20GCB:2:1:310:418/2
+AAAGATTAATGTCTCTAATTAATAATGCAAACCTTT
++
+AA<AAAAAAAAAAAAAAAAAAAAAAA5A>A><>???
+ at HWI-EAS_4_PE-FC20GCB:2:1:154:875/2
+CTGAGAAAGACATGAAACAACCATCATTCAGAAAAC
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAA<A<>%<?<
+ at HWI-EAS_4_PE-FC20GCB:2:1:339:736/2
+AGGTCAGCACGCTGTTTCTGGGCTTTTGCTACGCGC
++
+AAAAAAAAAAAAAAAAAAA???AAAAA=AA><(:::
+ at HWI-EAS_4_PE-FC20GCB:2:1:254:757/2
+CTATCGACTGGACCAAAGTGATCTTTAAAGGCTTTT
++
+AAAAAAAAAAAAAA?>?AAAAAAAAAA?*<6>>?%<
+ at HWI-EAS_4_PE-FC20GCB:2:1:426:791/2
+TTCGCTTTCAGTGGCGAACTTATGATTGATATAAAT
++
+AAAAAAAAA<AA9<AA<A&AA<A<9AA//A9?5559
+ at HWI-EAS_4_PE-FC20GCB:2:1:305:667/2
+TATAAATATTTTCACGTTGTCAGTTTGTTCGTTCTT
++
+AAAAAAAAAAAA?A+AAA;AAA;A&A8A*2:??7(?
+ at HWI-EAS_4_PE-FC20GCB:2:1:315:601/2
+AATATACCAAAGAGTGAAGTTGAAAGCCGATAGCAG
++
+AAAAAAAAAAAAAAAAAAAAAAAAA?AAA<></9<9
+ at HWI-EAS_4_PE-FC20GCB:2:1:275:625/2
+TAATTTTAGTTATGATTGCCTTGTCGGGTTTTGGAT
++
+AAAAAAAAAAAAA?AAA;AAAA3AA=77AA?&+%:?
+ at HWI-EAS_4_PE-FC20GCB:2:1:521:849/2
+TCTCATACCATGAGATAGTTATCTGAACCACCCTCA
++
+AAAAAAAAAAAAAA?AAAAA>AAA9A6<??>>9996
+ at HWI-EAS_4_PE-FC20GCB:2:1:299:561/2
+TAAAGACGTCATTGCAATTGATGGAAAAACGCTCCG
++
+AAAAAAAAAAAAAAAAAAA?AAA?AAAAAA::?<><
+ at HWI-EAS_4_PE-FC20GCB:2:1:109:205/2
+ACAATCCCCATGTCAGTACTTGCAAGATAGTCAATC
++
+AAAAAAAAAA5AAAA?AAAAA;AAA8AAA8??;3?;
+ at HWI-EAS_4_PE-FC20GCB:2:1:145:390/2
+AGATGGGTAAGGAAGAATTTTGCTCACGGAGTTTGC
++
+AAAAAAAAAAAA?AAAAAAAA9>9><A6A?6<>?/-
+ at HWI-EAS_4_PE-FC20GCB:2:1:294:549/2
+TTTCGTGACCAACGTAGATAAAGCTGCCGAAGCGGT
++
+AAAAAAAAAAAAAAA;A;AA9A>AAA?<6/9696</
+ at HWI-EAS_4_PE-FC20GCB:2:1:430:414/2
+ACATCCCGATGCGGCGTGTAAACCCATAATTTGTTT
++
+AAA3A*;3A;A3A.A;A;*..A7A3-166+;6)&;<
+ at HWI-EAS_4_PE-FC20GCB:2:1:242:635/2
+CTTCTCCTGCTAATTTCTCTGCCGCTTGTAGGGTAA
++
+AAAAAAAAAAAAAAAAAA;A>AAAAAA</A66+?6/
+ at HWI-EAS_4_PE-FC20GCB:2:1:492:569/2
+CGGGGCGCTGGTTTATCTGGTTGGGCTATGGATCTC
++
+AAAAAAAAAAAAAA1AAAA;AAA3?AAAAA::<<?6
+ at HWI-EAS_4_PE-FC20GCB:2:1:510:651/2
+TGAAAATATGGCTTTGAATAAGTAAAAGATGAAAGT
++
+AAAAAAA<AAAAAAA<AAAA<9AAAAA/5<<9>>/5
+ at HWI-EAS_4_PE-FC20GCB:2:1:294:569/2
+ATGCGACAATCACTTCAGGCTGCTTTACCTGAAATT
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA:>0?><
+ at HWI-EAS_4_PE-FC20GCB:2:1:287:885/2
+TCTCTGACTGTAAGCCAACAAAGTATGCCGACGATT
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA<<%<><
+ at HWI-EAS_4_PE-FC20GCB:2:1:268:712/2
+CCACACGGGCACCGACTGAAGTTCTGGTGTTATCAT
++
+AAAAAA<AAAAAAAAAAAAAAAAAAA5AA>?</5<<
+ at HWI-EAS_4_PE-FC20GCB:2:1:196:443/2
+GGCAGATGGTCATTGACCTCGGCATAGGTCAGATAG
++
+AAAAAAAAAAAAAAAAAAAAAAA>AAAAAA<:?>?<
+ at HWI-EAS_4_PE-FC20GCB:2:1:580:641/2
+CTGTGCAGCTTATTCTCCACGTGCCAGTGGTTTCGG
++
+AAA=AA=.AA=A9A=AA=A==93AA-;;6;<<<26+
+ at HWI-EAS_4_PE-FC20GCB:2:1:383:591/2
+CATCAGCCGTGAAGATCTGCACGCCGTGCTGACCGG
++
+AAAAAAAAAAAAA;?AAAAAAAAAA<<?AA9?>%66
+ at HWI-EAS_4_PE-FC20GCB:2:1:230:738/2
+AGATATAGTTACTTTTCCTTTGCCAATAATTGAAGA
++
+AAAAAAAAAAAAAAAAAAAAA;AAA=A==A?0+<06
+ at HWI-EAS_4_PE-FC20GCB:2:1:476:683/2
+TTGCGGTTCGTCACTGTGGATTTGGCTGGCAGCGGT
++
+AAAAAAAAAAAA3AA?A;A?AAA;AAA=*76+>*60
+ at HWI-EAS_4_PE-FC20GCB:2:1:394:610/2
+GAAAGCAACGTTACCGTGACCATCAAATACCAGGTT
++
+AAAAAAAAAAAAAAA?AAAAAAAAAAAA-A<>69<<
+ at HWI-EAS_4_PE-FC20GCB:2:1:268:893/2
+CTAACGGCAAAAACCAAAGGGAATCCTGACAGCTGG
++
+9-.99.AAAA39+3=A3+9933..=;3.366.;6;<
+ at HWI-EAS_4_PE-FC20GCB:2:1:245:483/2
+TGTCGAGCAAAGCAAAACAGGCGTAAAAATTGCCAT
++
+AAAAAAAAAAAAAAAAAAAAA>AAAAAAAA?9>6><
+ at HWI-EAS_4_PE-FC20GCB:2:1:184:640/2
+AAACTTAATGACGCTCACATTATCGACTTGACTTTT
++
+...&.+..+*..&*..*...*,..*...(....().
+ at HWI-EAS_4_PE-FC20GCB:2:1:169:676/2
+CCTGTTGTTTATGCACAGATTGCGTAACCAGAATAC
++
+AAAAAAAAAA<A<AAA<97AA9A1A>>AA599(><<
+ at HWI-EAS_4_PE-FC20GCB:2:1:537:477/2
+TGATGATTATTAATAAATGTCAAATATGAAAGAAAC
++
+AAAAAAAAAAAA?AA?AA;AAAAAAAA===<2?:6:
+ at HWI-EAS_4_PE-FC20GCB:2:1:383:774/2
+CATACTCAAGATCTTCATCTGTTGAAAAGGATTCAT
++
+AAAAAAAAAAAAAAAAAAAA>AAAAAA<<6>?6><?
+ at HWI-EAS_4_PE-FC20GCB:2:1:161:706/2
+CTGTACAACATCGTTCCTTACGGTATCGATGCTACC
++
+AAAAAA5?AAAAAAAAAAA;A;0??AA48A.<8<<8
+ at HWI-EAS_4_PE-FC20GCB:2:1:353:459/2
+AATCCCTTGTATATCAGTATTTATTTGTATCCAGAG
++
+AAAAAAAAAAAAAAAA?AAAAAAAAA2AAA<<>2?+
+ at HWI-EAS_4_PE-FC20GCB:2:1:383:678/2
+TTCAGCGCGCCTCCTTGATTATTATCATGGGTTGCG
++
+=AA.====39A9&A+&939A+A..=6;A%..2.22.
+ at HWI-EAS_4_PE-FC20GCB:2:1:390:661/2
+ATTTTCTAAACGAATTTTAAACGGCGTCATTTATAA
++
+AAAA=AA.AAAA..AAAA3AAA93A;AA*A<<&<<;
+ at HWI-EAS_4_PE-FC20GCB:2:1:406:796/2
+ACTGCCTTGTAAACTTACATCGCGTACACCAAGATG
++
+AAAAAAA5;A55+A?A?A&AA5A0?8A>*A88*<<.
+ at HWI-EAS_4_PE-FC20GCB:2:1:282:597/2
+CATCCTGAATAGCCAAACAATGGCAATGTTCCACTT
++
+AAAAAAAAAAAAAAA?AAAAAA;AAAAAAA>?6<>?
+ at HWI-EAS_4_PE-FC20GCB:2:1:204:474/2
+GGTGATGAACTGGAACTTGTAGCCCATATCCGACAG
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA?6?9>/
+ at HWI-EAS_4_PE-FC20GCB:2:1:151:368/2
+TGGTTATCTATTGCTTTAAAATTACCACTGGGCGTA
++
+..*&....................*.....&....,
+ at HWI-EAS_4_PE-FC20GCB:2:1:518:680/2
+AATGTGGGTAGCCAATGCGGCAACGATCGCGCCCTC
++
+A.=A3==AAAA=A+3==99AA9==.36A*6-;;%-2
+ at HWI-EAS_4_PE-FC20GCB:2:1:267:385/2
+TCTCCTGATGATGAATTGTTTTATTTAGTCCACTGT
++
+AAAAAAAAAAAAA+AAA?AAAAAAAAA7A=:6:?<+
+ at HWI-EAS_4_PE-FC20GCB:2:1:251:692/2
+GTTCATAAAACGCAAAACGATTGATGCGGATGATGT
++
+AAAAAAAAAAAAAAAAAAAAAAA>AAA<<?<99>>9
+ at HWI-EAS_4_PE-FC20GCB:2:1:84:839/2
+AATTATCAGTCAGGGATACAGGTATTGATACCTACG
++
+A5AAAAA5AAAAA??AAAAA??AAAA8888;;8<8.
+ at HWI-EAS_4_PE-FC20GCB:2:1:415:656/2
+CGACAATTCTGACGTCGGTAAAACCAGAGCAATATC
++
+AAAAAAAAAAAAAAAAAAAA>A>AAA6A6A<9<?><
+ at HWI-EAS_4_PE-FC20GCB:2:1:268:818/2
+AGTTTTCGGGCCTCATCCCGTTTTGCACGAGCTTCG
++
+A;A3AAA*;;AAAA3AAAA;7A;.7A1A.-1<<;<.
+ at HWI-EAS_4_PE-FC20GCB:2:1:188:845/2
+GGACTCAATGTCCCCATTTGTAAATGGCTATGCTTA
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAAAA=<0>>?:
+ at HWI-EAS_4_PE-FC20GCB:2:1:152:689/2
+GTCGTGCCTGGTCTACTAGTCGTAAAAATTGACCGC
++
+AAAAAAAAAAAAAA&AA:8AA9AA1???<A664</<
+ at HWI-EAS_4_PE-FC20GCB:2:1:290:530/2
+CATCTCTACATTGATTATGAGTATTCAGAAATTCCT
++
+AAAAAAA<AAAAA7AA<AAA9AAAAA<5<5<?>>>?
+ at HWI-EAS_4_PE-FC20GCB:2:1:198:672/2
+ATGGAATGGCAACTTTCATTCCTTTTTTTAATGTTT
++
+5AAAAAA??AA;AAAAA5AAAAAAAAAAA8-?+<??
+ at HWI-EAS_4_PE-FC20GCB:2:1:378:827/2
+CGTGACCGATATGACAGAGATCGTAAACGGTGATTC
++
+A<AAAAAAAAAAAAAAA<AAAAAAAA>AAA<9?>??
+ at HWI-EAS_4_PE-FC20GCB:2:1:330:467/2
+CCCAGGAAGTTGCAGAACAAGCAGAACCGGGGGTTG
++
+AAAAAAAAAAAAAAAA?>AAA>>A?AAA?</<?69/
+ at HWI-EAS_4_PE-FC20GCB:2:1:601:561/2
+AGATTAAAATATAAGGTTCTTTAGCAGTTCTTTAGG
++
+AAAAAA9.AA.A39=9AA3AAA=.936AAA<<(2+.
+ at HWI-EAS_4_PE-FC20GCB:2:1:426:665/2
+AAGCCATTAAGGCAAAACTGGCGGAATTACAGCCAT
++
+AAAAAAAAAAAAA??AAAAAAA?AAAAA%A>6<>::
+ at HWI-EAS_4_PE-FC20GCB:2:1:173:732/2
+TGTTTTTGCCATGATCGTGCCTTGAGTGAATAATTG
++
+AAAAAAAAAAAAA?AA?AAAAAA9<AA?6:?96<?6
+ at HWI-EAS_4_PE-FC20GCB:2:1:284:789/2
+GTGCATCAGATTCTGTACGGAGAAAATATCGTCAAG
++
+5;AAAAA????5AA?A1A;1+5;A?8A8AA4/<;;+
+ at HWI-EAS_4_PE-FC20GCB:2:1:91:525/2
+TTGGAGAACGTCAGGAGAGGCATTTTGGCAGATCAC
++
+AAAAAAAAAAAAAAAA?1+AA8AAAA66A669<<9<
+ at HWI-EAS_4_PE-FC20GCB:2:1:553:711/2
+CATTACTCTTTATTAAGGAATTTTACTGCCTTATCA
++
+AAAAAAAAAAAAAAAA;;AAAAAAAAA8==????<+
+ at HWI-EAS_4_PE-FC20GCB:2:1:86:239/2
+AAGATGTGGAAAATGCACGTCATTCATTTCGTCATT
++
+AAAAAAAAAAA<AAAAAAAAAAAAA<AAA>5>85??
+ at HWI-EAS_4_PE-FC20GCB:2:1:343:767/2
+ACCAATAAGTTGATTGAACTCGCCTTTGGTCGCGTG
++
+AAAAAAA.AA9AAA3AAAA=A=AAA;A+;;<6<;62
+ at HWI-EAS_4_PE-FC20GCB:2:1:387:326/2
+GGCAAAGTTAAAGCCATGCATTATATGAGTGATAAC
++
+AAAAAAAAAAAAAAAAAAAAAAAAAA=A=A<00:<6
+ at HWI-EAS_4_PE-FC20GCB:2:1:185:656/2
+TTTCTTTCGGCAGCCATGGCATGGGCCGATACTGAA
++
+AAAAAAAA<<AAAAAAA<<A<A1<9></<>04>/--
+ at HWI-EAS_4_PE-FC20GCB:2:1:192:634/2
+TTCCGTGGCGCTCATCAACGTCGGTTTATCCCCCAT
++
+AAAAAAAAAAAAAAAAAAA?AAAAAAA+=7<:<6*<
+ at HWI-EAS_4_PE-FC20GCB:2:1:210:740/2
+CCGACCGGGATTATCTCCGCATTCGCCTTTACCGGT
++
+AAAAAAAAAAAAAAAAAAAA8AAAAABA5=<:?:0?
+ at HWI-EAS_4_PE-FC20GCB:2:1:210:630/2
+TAATGAAAAAGATATAAATTATGGGGTGGAAATAGA
++
+AAAAAAAAAAAAAAAAAAAAAA?A?7AA2A<<??:<
+ at HWI-EAS_4_PE-FC20GCB:2:1:411:681/2
+AGAGCTTCGCCACTCAACTTAAGCAGAATGCGTTTA
++
+AA<AAAAAAAAAA9AA<A9A<<AAAA5>>A?99?<<
+ at HWI-EAS_4_PE-FC20GCB:2:1:585:657/2
+TCAAATTTTAACCGAATTCAACTGTTTTATCATTGA
++
+AAAAAAAAAAAAA?AAAAAAAAAAAAAAAA><??96
+ at HWI-EAS_4_PE-FC20GCB:2:1:63:801/2
+TATAGTTACTTTTCCTTTGCCAATAATTGAAGAATA
++
+AAAAAAAAAAAAAAAAAA;AA9?AAAAA7A:6*<?<
+ at HWI-EAS_4_PE-FC20GCB:2:1:185:700/2
+CAAATCCAGATTGTTGTGTTGTTGCCATGGTATTCT
++
+AA<AAAAAAAAAAAA<AAAA<AA1AA5A/+?5<>><
+ at HWI-EAS_4_PE-FC20GCB:2:1:292:584/2
+TTGCCAAAACGTCTGACTGAGGCAGGCATCAGGAAT
++
+AAAAAAAAAAAAAAAAAAAAAAA?AAA7A=::>><:
+ at HWI-EAS_4_PE-FC20GCB:2:1:391:779/2
+TATGACGTTGTTGATGATATAAGGAAAGATTCTAAA
++
+.......&.....*..............,.......
+ at HWI-EAS_4_PE-FC20GCB:2:1:346:503/2
+GCAGTCACGTAATCTTCGTCATAGAACATGGCTTCT
++
+AA7AAA*AAA3AAAAAA33A7AA37AA;116;<;6%
+ at HWI-EAS_4_PE-FC20GCB:2:1:253:837/2
+CAGCGCCCTTCTTTCCACGCATACTGGGCGCTGTTG
++
+.&..................................
+ at HWI-EAS_4_PE-FC20GCB:2:1:214:402/2
+GGTTAAACAGCTGACGATCAGGGCGATTTACATCGC
++
+AAAAAA.A77*A;&A;AA;A;7AAAAAA%A<;<86<
+ at HWI-EAS_4_PE-FC20GCB:2:1:548:624/2
+GGTCATGGTGTTTCCTTCTTATGATATGCAGTTGAT
++
+AAAAAAAA<AAAAAAAAAAAAA9<A>A<><5&(+9<
+ at HWI-EAS_4_PE-FC20GCB:2:1:73:597/2
+CATCAGGATTGCCATCAGGATCATTTGATTGCGTAA
++
+AAAAAAAAAAAAAAAAAA?AAAAAAAAAAA/>/<>6
+ at HWI-EAS_4_PE-FC20GCB:2:1:543:793/2
+TAGCTCCCGTAGTAATCGACAATAAGAGAAACAATG
++
+AAAAAAAAAA5?AA?AA?5A;0A5;A>84888;8?<
+ at HWI-EAS_4_PE-FC20GCB:2:1:240:771/2
+AGAAATGACATTATCTTTGAGGAATATGCCCTTATT
++
+AAAAAAAAAAAAAAAAAA?391A>A?A?AA<>>/?<
+ at HWI-EAS_4_PE-FC20GCB:2:1:118:528/2
+TTATGGTTACTTGCAGATCACCACCATTGGCCGCAG
++
+AAAAAAA?5AAA?A?1?AA;?A6?A8AA..;4.4(4
+ at HWI-EAS_4_PE-FC20GCB:2:1:368:774/2
+CTGTTGCATTATTCAAAAAGCAACCCAATTAGTGCA
++
+AAAAAAAAAAAAAA+AAA3AAAAAAAA=AA::6:?<
+ at HWI-EAS_4_PE-FC20GCB:2:1:290:601/2
+CCACAATTTGAAGGCGGCTCATGCGCATCATCTTTT
++
+AAAAAAAAAAAAAAAA?AAAAA>>>AAA??>>9?<?
+ at HWI-EAS_4_PE-FC20GCB:2:1:128:645/2
+GTTTAGCTACGCAGGATTATGCAAGCTGGCCCACGC
++
+AAAAAAAAAAAAAA?AAAAA9AAA>AA<<??<?<6<
+ at HWI-EAS_4_PE-FC20GCB:2:1:540:680/2
+AAACACTCCCCAGCAACTGACAGACAAAGATTTATT
++
+AAAAAAAAAAAAAA;AAAAAAAAAAA2AAA>>><?<
+ at HWI-EAS_4_PE-FC20GCB:2:1:213:489/2
+AGTTGCTGGGCCTGCCGTACCGTAAAATCATCCTTT
++
+AAAAAAAAA<AAAAAAAAA<A<AA9<<A<>?/4???
+ at HWI-EAS_4_PE-FC20GCB:2:1:490:531/2
+TATTTTTTTATTCACGACACTGTTTCTGCTTTCTTC
++
+A;3AA;*AA;A7AAA77A.A73;A;;;.-A<<-<),
+ at HWI-EAS_4_PE-FC20GCB:2:1:419:475/2
+CGGTCGATTCAGCAAAAACGGTTGGCTTAGTGAGTT
++
+AAAAAAAAAAAAAAAAAAAAAAAAAAA=A2<2?20?
+ at HWI-EAS_4_PE-FC20GCB:2:1:326:304/2
+CTAAAGATGAAAATTATTAGAGTCGCATTAAAAATG
++
+AAAAAA5AAA;A;AAAAAA;?;AA;AAA>88;4<?4
+ at HWI-EAS_4_PE-FC20GCB:2:1:201:683/2
+GAAGAACAACAGCGGGGGATTGAGCAGGTTGCACAG
++
+AAAA<AAAAAAAAAAAAA<AAAAAA<<>4>9<-945
+ at HWI-EAS_4_PE-FC20GCB:2:1:126:737/2
+ACATTCTTCGTCACATCCCAGGTCGCGCTCAGGCCA
++
+AAAAAAAAA<AAAAAAAAA<<<@AAA>A<A>/5?>?
+ at HWI-EAS_4_PE-FC20GCB:2:1:350:588/2
+GGTACAAAATAGATGCTGGACTCTCCGAATCCTATA
++
+;?5AAAAAAAAAA?A??;?AA;AAA>AAAA?4?844
+


=====================================
debian/tests/ref/cns.cns.summary
=====================================
@@ -0,0 +1,15 @@
+N_REF: 1
+REF_NAME:|MYDB|1 this is sequence 1
+GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG
+TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA
+GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT
+GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG
+GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT
+TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG
+CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT
+TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT
+CACAGACAGCCTGAGACAGTTCTTACGGAAACACCCCAGGACACAATTGAATTAAACAGATTGAATTTAGAATCTTCCAA
+
+
+REF_LENGTH:0
+REF_OFFSET:766


=====================================
debian/tests/ref/cns.cns.zr
=====================================
Binary files /dev/null and b/debian/tests/ref/cns.cns.zr differ


=====================================
debian/tests/ref/maqindex1/part1.map.vm
=====================================
Binary files /dev/null and b/debian/tests/ref/maqindex1/part1.map.vm differ


=====================================
debian/tests/ref/maqindex1/part1.map.zr
=====================================
Binary files /dev/null and b/debian/tests/ref/maqindex1/part1.map.zr differ


=====================================
debian/tests/ref/maqindex2/cns.cns.summary
=====================================
@@ -0,0 +1,15 @@
+N_REF: 1
+REF_NAME:|MYDB|1 this is sequence 1
+GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG
+TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA
+GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT
+GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG
+GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT
+TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG
+CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT
+TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT
+CACAGACAGCCTGAGACAGTTCTTACGGAAACACCCCAGGACACAATTGAATTAAACAGATTGAATTTAGAATCTTCCAA
+
+
+REF_LENGTH:0
+REF_OFFSET:766


=====================================
debian/tests/ref/maqindex2/cns.cns.zr
=====================================
Binary files /dev/null and b/debian/tests/ref/maqindex2/cns.cns.zr differ


=====================================
debian/tests/ref/maqindex2/part1.map.vm
=====================================
Binary files /dev/null and b/debian/tests/ref/maqindex2/part1.map.vm differ


=====================================
debian/tests/ref/maqindex2/part1.map.zr
=====================================
Binary files /dev/null and b/debian/tests/ref/maqindex2/part1.map.zr differ


=====================================
debian/tests/ref/maqindex3/cns.cns.summary
=====================================
@@ -0,0 +1,15 @@
+N_REF: 1
+REF_NAME:|MYDB|1 this is sequence 1
+GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG
+TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA
+GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT
+GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG
+GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT
+TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG
+CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT
+TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT
+CACAGACAGCCTGAGACAGTTCTTACGGAAACACCCCAGGACACAATTGAATTAAACAGATTGAATTTAGAATCTTCCAA
+
+
+REF_LENGTH:0
+REF_OFFSET:766


=====================================
debian/tests/ref/maqindex3/cns.cns.zr
=====================================
Binary files /dev/null and b/debian/tests/ref/maqindex3/cns.cns.zr differ


=====================================
debian/tests/ref/part1.map.vm
=====================================
Binary files /dev/null and b/debian/tests/ref/part1.map.vm differ


=====================================
debian/tests/ref/part1.map.zr
=====================================
Binary files /dev/null and b/debian/tests/ref/part1.map.zr differ


=====================================
debian/tests/ref/test.fa.gz.zr
=====================================
Binary files /dev/null and b/debian/tests/ref/test.fa.gz.zr differ


=====================================
debian/tests/ref/zrio.use.out
=====================================
@@ -0,0 +1,11 @@
+>gnl|MYDB|1 this is sequence 1
+GAATTCCCGCTACAGGGGGGGCCTGAGGCACTGCAGAAAGTGGGCCTGAGCCTCGAGGATGACGGTGCTGCAGGAACCCG
+TCCAGGCTGCTATATGGCAAGCACTAAACCACTATGCTTACCGAGATGCGGTTTTCCTCGCAGAACGCCTTTATGCAGAA
+GTACACTCAGAAGAAGCCTTGTTTTTACTGGCAACCTGTTATTACCGCTCAGGAAAGGCATATAAAGCATATAGACTCTT
+GAAAGGACACAGTTGTACTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGCAAGCTTGCAGAAG
+GGGAACAAATCTTATCTGGTGGAGTGTTTAATAAGCAGAAAAGCCATGATGATATTGTTACTGAGTTTGGTGATTCAGCT
+TGCTTTACTCTTTCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAGGATCAGAATGTTACCAAAAGAG
+CCTTAGTTTAAATCCTTTCCTCTGGTCTCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTGACCAAACAT
+TTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAACACAAGTACCTAATCATAGTTTATCT
+CACAGACAGCCTGAGACAGTTCTTACGGAAACACCCCAGGACACAATTGAATTAAACAGATTGAATTTAGAATCTTCCAA
+


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,76 @@
+#!/bin/bash
+set -e
+
+pkg=maqview
+
+export LC_ALL=C.UTF-8
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  # Double quote below to expand the temporary directory variable now versus
+  # later is on purpose.
+  # shellcheck disable=SC2064
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+gunzip -r *
+ls -R
+cd data
+echo -e "\e[93m\e[1mPREP INPUT FILES FOR MAQVIEW\e[0m"
+maq fasta2bfa test.fa test.bfa
+echo 1
+maq fastq2bfq test.fastq part1.bfq
+echo 2
+maq fastq2bfq test.fastq part2.bfq
+echo 3
+maq map part1.map test.fa part1.bfq
+echo 4
+maq map part2.map test.fa  part2.bfq
+echo 5
+maq mapmerge aln.map part1.map part2.map
+echo 6
+maq assemble cns.cns test.fa aln.map
+echo 7
+gzip test.fa
+echo -e "\e[92m\e[1mDone\e[0m"
+echo
+
+#do_stuff_to_test_package#
+echo -e "\e[93m\e[1mTest 1\e[0m"
+zrio make test.fa.gz
+diff test.fa.gz.zr ../ref/test.fa.gz.zr
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 2\e[0m"
+zrio use test.fa.gz 0 > zrio.use.out
+diff zrio.use.out ../ref/zrio.use.out
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 3\e[0m"
+maqindex -i part1.map
+diff part1.map.vm ../ref/maqindex1/part1.map.vm
+diff part1.map.zr ../ref/maqindex1/part1.map.zr
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 4\e[0m"
+maqindex -c cns.cns -i part1.map
+diff part1.map.vm ../ref/maqindex2/part1.map.vm
+diff part1.map.zr ../ref/maqindex2/part1.map.zr
+diff cns.cns.zr ../ref/maqindex2/cns.cns.zr
+diff cns.cns.summary ../ref/maqindex2/cns.cns.summary
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 5\e[0m"
+maqindex -i -c cns.cns
+diff cns.cns.zr ../ref/maqindex3/cns.cns.zr
+diff cns.cns.summary ../ref/maqindex3/cns.cns.summary
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+



View it on GitLab: https://salsa.debian.org/med-team/maqview/-/compare/412d0b1164d335ed17e6a84b4765558561b96184...6ae8c65c86500d9a4457ff60358dac817a3a4e7b

-- 
View it on GitLab: https://salsa.debian.org/med-team/maqview/-/compare/412d0b1164d335ed17e6a84b4765558561b96184...6ae8c65c86500d9a4457ff60358dac817a3a4e7b
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