[med-svn] [Git][med-team/flash][master] 3 commits: Add test and reference data

[Pranav Ballaney]

Pranav Ballaney pushed to branch master at Debian Med / flash


Commits:
584f55fc by Pranav Ballaney at 2020-06-17T05:37:20+05:30
Add test and reference data

- - - - -
05215e02 by Pranav Ballaney at 2020-06-17T05:37:40+05:30
Add autopkgtests

- - - - -
1ccea99f by Pranav Ballaney at 2020-06-17T05:42:53+05:30
Install docs

- - - - -


11 changed files:

- + debian/README.test
- debian/changelog
- debian/docs
- + debian/examples
- + debian/tests/control
- + debian/tests/data/README.test_data
- + debian/tests/data/frag_1.fastq
- + debian/tests/data/frag_2.fastq
- + debian/tests/data/ref/out.hist
- + debian/tests/data/ref/out.histogram
- + 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 +1,11 @@
+flash (1.2.11-2) UNRELEASED; urgency=medium
+
+  * Add test and reference data
+  * Add autopkgtests
+  * Install docs
+
+ -- Pranav Ballaney <ballaneypranav at gmail.com>  Wed, 17 Jun 2020 05:37:47 +0530
+
 flash (1.2.11-1) unstable; urgency=medium
 
   * Initial release (Closes: #961587)


=====================================
debian/docs
=====================================
@@ -1 +1,4 @@
 README*
+debian/README*
+debian/tests/run-unit-test
+debian/tests/data/README*
\ No newline at end of file


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


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


=====================================
debian/tests/data/README.test_data
=====================================
@@ -0,0 +1,6 @@
+Files: frag* 
+Source: The "No Error" dataset for Flash, avaiable at http://ccb.jhu.edu/software/FLASH/
+Direct URL: http://ccb.jhu.edu/software/FLASH/noError.tar.gz
+
+Files: ref/*
+Source: Produced by running Flash on the reads described above.
\ No newline at end of file


=====================================
debian/tests/data/frag_1.fastq
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/tests/data/frag_2.fastq
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/tests/data/ref/out.hist
=====================================
@@ -0,0 +1,64 @@
+121	1
+125	2
+126	3
+128	2
+131	4
+132	1
+133	3
+134	3
+135	3
+136	3
+137	4
+138	2
+139	6
+140	7
+141	6
+142	4
+143	6
+144	3
+145	6
+146	7
+147	6
+148	5
+149	9
+150	12
+151	7
+152	7
+153	10
+154	12
+155	14
+156	9
+157	9
+158	14
+159	15
+160	13
+161	18
+162	14
+163	14
+164	13
+165	18
+166	19
+167	13
+168	17
+169	11
+170	19
+171	24
+172	22
+173	26
+174	18
+175	24
+176	22
+177	23
+178	26
+179	32
+180	26
+181	20
+182	22
+183	18
+184	22
+185	23
+186	27
+187	30
+188	26
+189	18
+190	22


=====================================
debian/tests/data/ref/out.histogram
=====================================
@@ -0,0 +1,70 @@
+121	**
+122	
+123	
+124	
+125	****
+126	******
+127	
+128	****
+129	
+130	
+131	*********
+132	**
+133	******
+134	******
+135	******
+136	******
+137	*********
+138	****
+139	*************
+140	***************
+141	*************
+142	*********
+143	*************
+144	******
+145	*************
+146	***************
+147	*************
+148	***********
+149	********************
+150	***************************
+151	***************
+152	***************
+153	**********************
+154	***************************
+155	*******************************
+156	********************
+157	********************
+158	*******************************
+159	*********************************
+160	*****************************
+161	****************************************
+162	*******************************
+163	*******************************
+164	*****************************
+165	****************************************
+166	******************************************
+167	*****************************
+168	**************************************
+169	************************
+170	******************************************
+171	******************************************************
+172	*************************************************
+173	**********************************************************
+174	****************************************
+175	******************************************************
+176	*************************************************
+177	***************************************************
+178	**********************************************************
+179	************************************************************************
+180	**********************************************************
+181	*********************************************
+182	*************************************************
+183	****************************************
+184	*************************************************
+185	***************************************************
+186	************************************************************
+187	*******************************************************************
+188	**********************************************************
+189	****************************************
+190	*************************************************


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,26 @@
+#!/bin/bash
+set -e
+
+pkg=flash
+
+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 *
+flash frag_1.fastq frag_2.fastq 2>&1 | tee flash.log
+
+for f in out.hist*
+do
+  echo Comparing $f ref/$f
+  diff -y --suppress-common-lines $f ref/$f
+done
\ No newline at end of file



View it on GitLab: https://salsa.debian.org/med-team/flash/-/compare/36402d4b8b1403feda8aae690bc4b3f2f6bca83e...1ccea99f8780cfd5cc2fef10e05b87a487461ee9

-- 
View it on GitLab: https://salsa.debian.org/med-team/flash/-/compare/36402d4b8b1403feda8aae690bc4b3f2f6bca83e...1ccea99f8780cfd5cc2fef10e05b87a487461ee9
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