[med-svn] [Git][med-team/ivar][master] 4 commits: Add reference data for autopkgtests

Pranav Ballaney gitlab at salsa.debian.org
Tue Jun 16 17:28:04 BST 2020 


Pranav Ballaney pushed to branch master at Debian Med / ivar


Commits:
06ee9d1c by Pranav Ballaney at 2020-06-16T21:52:59+05:30
Add reference data for autopkgtests

- - - - -
faee7440 by Pranav Ballaney at 2020-06-16T21:53:14+05:30
Add recommended package as per docs

- - - - -
a2f912c4 by Pranav Ballaney at 2020-06-16T21:53:47+05:30
Add autopkgtests

- - - - -
355391c7 by Pranav Ballaney at 2020-06-16T21:56:26+05:30
Install docs and examples

- - - - -


16 changed files:

- + debian/README.test
- debian/changelog
- debian/control
- + debian/examples
- debian/ivar.docs
- + debian/tests/control
- + debian/tests/ref/README.test_data
- + debian/tests/ref/out-consensus.fa
- + debian/tests/ref/out-consensus.qual.txt
- + debian/tests/ref/out-filtered.tsv
- + debian/tests/ref/out-getmasked.txt
- + debian/tests/ref/out-removereads.sam
- + debian/tests/ref/out-trim.sam
- + debian/tests/ref/out-trim2.sam
- + debian/tests/ref/out-variants.tsv
- + 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 +1,12 @@
+ivar (1.2.2+dfsg-3) UNRELEASED; urgency=medium
+
+  * Add reference data for autopkgtests
+  * Add recommended package as per docs
+  * Add autopkgtests
+  * Install docs and examples
+
+ -- Pranav Ballaney <ballaneypranav at gmail.com>  Tue, 16 Jun 2020 21:55:42 +0530
+
 ivar (1.2.2+dfsg-2) unstable; urgency=medium
 
   * debhelper-compat 13 (routine-update)


=====================================
debian/control
=====================================
@@ -15,6 +15,7 @@ Package: ivar
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends}
+Recommends: samtools
 Description: functions broadly useful for viral amplicon-based sequencing
  iVar is a computational package that contains functions broadly useful
  for viral amplicon-based sequencing. Additional tools for metagenomic


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


=====================================
debian/ivar.docs
=====================================
@@ -1,2 +1,6 @@
+README*
 docs/COOKBOOK.md
 docs/MANUAL.md
+debian/README*
+debian/tests/run-unit-test
+debian/tests/ref/README*
\ No newline at end of file


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


=====================================
debian/tests/ref/README.test_data
=====================================
@@ -0,0 +1,2 @@
+The files used as references for testing were obtained by running the software on
+the data provided in the testdata folder with this package.
\ No newline at end of file


=====================================
debian/tests/ref/out-consensus.fa
=====================================
@@ -0,0 +1,2 @@
+>Consensus_out-consensus_threshold_0_quality_20
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN


=====================================
debian/tests/ref/out-consensus.qual.txt
=====================================
@@ -0,0 +1 @@
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


=====================================
debian/tests/ref/out-filtered.tsv
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/tests/ref/out-getmasked.txt
=====================================
@@ -0,0 +1 @@
+WNV_400_2_LEFT	WNV_400_2_LEFT_alt	WNV_400_1_LEFT	WNV_400_1_LEFT_alt	WNV_400_3_LEFT
\ No newline at end of file


=====================================
debian/tests/ref/out-removereads.sam
=====================================
@@ -0,0 +1,2 @@
+test_20_381_1:0:0_6:0:0_1_150	163	test	31	60	11S139M	=	232	362	CTGCTGGGTCATGGGCCCATCATGATGGTCTTGGCGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCATCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAGAAAGAT	<>VG?UM[8R5:A7PL<>5AL>RZ5BH[EDFOUP?VHRHJ<UVE:NQ at WZ6VQMQ?9Y?L7ORM6BF=QBGJXBNCLENRXCRJZXN9 at GQ8N7U;YF[MJFTQF[FZCM>TNDXGK\=AIZW=X=V?;7K:7A<JDUTJSTGFES5\D;	RG:Z:Paired_Group_1_assembled_against_test	XA:i:0
+test_20_381_1:0:0_6:0:0_1_150	83	test	232	60	1M3D112M2D3M29S	=	20	-357	TGTCGGAATTGTTGGCCTCCTGCTGACCACAGCTATGGCAGCGGAGGTCACTAGACGTGGGAGTGCATACTATATGTACTTGGACTGAAACGATGCGGGGGAGGCCATATCTTCCAACCACATTGGGGTTGAATAAGTGGTTGAT	;SEFGTSJTUDJ<A7:K7;?V=X=WZIA=\KGXDNT>MCZF[FQTFJM[FY;U7N8QG at 9NXZJRCXRNELCNBXJGBQ=FB6MRO7L?Y9?QMQV6ZW at QN:EVU<JHRHV?OFDE[HB5ZR>LA5><LP7A:5R8[MU?GV><	RG:Z:Paired_Group_1_assembled_against_test	XA:i:7


=====================================
debian/tests/ref/out-trim.sam
=====================================
@@ -0,0 +1,2 @@
+test_20_381_1:0:0_6:0:0_1_150	163	test	31	60	11S139M	=	232	362	CTGCTGGGTCATGGGCCCATCATGATGGTCTTGGCGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCATCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAGAAAGAT	<>VG?UM[8R5:A7PL<>5AL>RZ5BH[EDFOUP?VHRHJ<UVE:NQ at WZ6VQMQ?9Y?L7ORM6BF=QBGJXBNCLENRXCRJZXN9 at GQ8N7U;YF[MJFTQF[FZCM>TNDXGK\=AIZW=X=V?;7K:7A<JDUTJSTGFES5\D;	RG:Z:Paired_Group_1_assembled_against_test	XA:i:0
+test_20_381_1:0:0_6:0:0_1_150	83	test	232	60	1M3D112M2D3M29S	=	20	-357	TGTCGGAATTGTTGGCCTCCTGCTGACCACAGCTATGGCAGCGGAGGTCACTAGACGTGGGAGTGCATACTATATGTACTTGGACTGAAACGATGCGGGGGAGGCCATATCTTCCAACCACATTGGGGTTGAATAAGTGGTTGAT	;SEFGTSJTUDJ<A7:K7;?V=X=WZIA=\KGXDNT>MCZF[FQTFJM[FY;U7N8QG at 9NXZJRCXRNELCNBXJGBQ=FB6MRO7L?Y9?QMQV6ZW at QN:EVU<JHRHV?OFDE[HB5ZR>LA5><LP7A:5R8[MU?GV><	RG:Z:Paired_Group_1_assembled_against_test	XA:i:7


=====================================
debian/tests/ref/out-trim2.sam
=====================================
@@ -0,0 +1,2 @@
+test_20_381_1:0:0_6:0:0_1_150	163	test	31	60	11S139M	=	232	362	CTGCTGGGTCATGGGCCCATCATGATGGTCTTGGCGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCATCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAGAAAGAT	<>VG?UM[8R5:A7PL<>5AL>RZ5BH[EDFOUP?VHRHJ<UVE:NQ at WZ6VQMQ?9Y?L7ORM6BF=QBGJXBNCLENRXCRJZXN9 at GQ8N7U;YF[MJFTQF[FZCM>TNDXGK\=AIZW=X=V?;7K:7A<JDUTJSTGFES5\D;	RG:Z:Paired_Group_1_assembled_against_test	XA:i:0
+test_20_381_1:0:0_6:0:0_1_150	83	test	232	60	1M3D112M2D3M29S	=	20	-357	TGTCGGAATTGTTGGCCTCCTGCTGACCACAGCTATGGCAGCGGAGGTCACTAGACGTGGGAGTGCATACTATATGTACTTGGACTGAAACGATGCGGGGGAGGCCATATCTTCCAACCACATTGGGGTTGAATAAGTGGTTGAT	;SEFGTSJTUDJ<A7:K7;?V=X=WZIA=\KGXDNT>MCZF[FQTFJM[FY;U7N8QG at 9NXZJRCXRNELCNBXJGBQ=FB6MRO7L?Y9?QMQV6ZW at QN:EVU<JHRHV?OFDE[HB5ZR>LA5><LP7A:5R8[MU?GV><	RG:Z:Paired_Group_1_assembled_against_test	XA:i:7


=====================================
debian/tests/ref/out-variants.tsv
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,66 @@
+#!/bin/bash
+set -e
+
+pkg=ivar
+
+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
+#do_stuff_to_test_package#
+echo -e "\e[93m\e[1mTest 1\e[0m"
+ivar trim -i data/test.sorted.bam -b data/test.bed -p out-trim
+samtools view out-trim.bam > out-trim.sam
+diff out-trim.sam ref/out-trim.sam
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 2\e[0m"
+ivar trim -i data/test.sorted.bam -b data/test.bed -p out-trim2 -q 15 -m 50 -s 4
+samtools view out-trim2.bam > out-trim2.sam
+diff out-trim2.sam ref/out-trim2.sam
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 3\e[0m"
+samtools mpileup -A -d 600000 -B -Q 0 data/test.trimmed.sorted.bam | ivar variants -p out-variants -q 20 -t 0.03
+diff out-variants.tsv ref/out-variants.tsv
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 4\e[0m"
+ivar filtervariants -t 0.5 -p out-filtered out-variants.tsv
+diff out-variants.tsv ref/out-variants.tsv
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 5\e[0m"
+samtools mpileup -d 1000 -A -Q 0 data/test.sorted.bam | ivar consensus -p out-consensus -q 20 -t 0
+diff out-consensus.qual.txt ref/out-consensus.qual.txt
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 6\e[0m"
+ivar getmasked -i data/test.filtered.tsv -b data/test.bed  -f data/out-filtered.tsv -p out-getmasked
+diff out-getmasked.txt ref/out-getmasked.txt
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 7\e[0m"
+ivar removereads -i out-trim.bam -p out-removereads -t data.out-getmasked.txt -b data/test.bed
+samtools view out-removereads.bam > out-removereads.sam
+diff out-removereads.sam ref/out-removereads.sam
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+



View it on GitLab: https://salsa.debian.org/med-team/ivar/-/compare/ae1b6fbe655eef81df454f9d386813c9965133ef...355391c7b2a4ca9f268d146488cc2e64111eb241

-- 
View it on GitLab: https://salsa.debian.org/med-team/ivar/-/compare/ae1b6fbe655eef81df454f9d386813c9965133ef...355391c7b2a4ca9f268d146488cc2e64111eb241
You're receiving this email because of your account on salsa.debian.org.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20200616/2ad96380/attachment-0001.html>

More information about the debian-med-commit mailing list