[med-svn] [Git][med-team/freebayes][master] 3 commits: Install test data
Pranav Ballaney
gitlab at salsa.debian.org
Sun May 31 22:22:07 BST 2020
Pranav Ballaney pushed to branch master at Debian Med / freebayes
Commits:
2e835cf7 by Pranav Ballaney at 2020-06-01T02:49:29+05:30
Install test data
- - - - -
e0bfd41e by Pranav Ballaney at 2020-06-01T02:49:59+05:30
Add autopkgtests
- - - - -
b1333211 by Pranav Ballaney at 2020-06-01T02:51:30+05:30
Install docs and binaries
- - - - -
16 changed files:
- + debian/README.test
- debian/changelog
- debian/docs
- + debian/examples
- + debian/source/include-binaries
- + debian/tests/control
- + debian/tests/data/README.test_data
- + debian/tests/data/targets.bed
- + debian/tests/data/test.alt
- + debian/tests/data/test.bam
- + debian/tests/data/test.bam.bai
- + debian/tests/data/test.bed
- + debian/tests/data/test.ref
- + debian/tests/data/test.ref.fai
- + debian/tests/data/test.vcf
- + 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 @@
+freebayes (1.3.2-3) UNRELEASED; urgency=medium
+
+ * Install test data
+ * Add autopkgtests
+ * Install docs and binaries
+
+ -- Pranav Ballaney <ballaneypranav at gmail.com> Mon, 01 Jun 2020 02:50:39 +0530
+
freebayes (1.3.2-2) unstable; urgency=medium
* Team upload.
=====================================
debian/docs
=====================================
@@ -1 +1,4 @@
README.md
+debian/README.test
+debian/tests/run-unit-test
+debian/tests/data/README*
\ No newline at end of file
=====================================
debian/examples
=====================================
@@ -0,0 +1,3 @@
+test/*
+examples/*
+debian/tests/data/*
\ No newline at end of file
=====================================
debian/source/include-binaries
=====================================
@@ -0,0 +1 @@
+debian/tests/data/test.bed*
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
=====================================
debian/tests/data/README.test_data
=====================================
@@ -0,0 +1 @@
+These test files were derived from the build time tests that come with the package.
\ No newline at end of file
=====================================
debian/tests/data/targets.bed
=====================================
@@ -0,0 +1,20 @@
+q 180 191
+q 1002 1013
+q 1811 1825
+q 1911 1922
+q 2344 2355
+q 2630 2635
+q 3250 3268
+q 4443 4454
+q 5003 5014
+q 5074 5085
+q 5089 5100
+q 5632 5646
+q 6412 6423
+q 8840 8851
+q 9245 9265
+q 9785 9796
+q 10526 10537
+q 11255 11266
+q 11530 11541
+q 12119 12130
=====================================
debian/tests/data/test.alt
=====================================
@@ -0,0 +1,2 @@
+>alt
+GTTAGGTTAAC
=====================================
debian/tests/data/test.bam
=====================================
Binary files /dev/null and b/debian/tests/data/test.bam differ
=====================================
debian/tests/data/test.bam.bai
=====================================
Binary files /dev/null and b/debian/tests/data/test.bam.bai differ
=====================================
debian/tests/data/test.bed
=====================================
@@ -0,0 +1,5 @@
+ref 0 1 first_base
+ref 2 4 third_and_fourth_base
+ref 5 6 sixth_base
+ref 7 8 eighth_base
+ref 10 11 eleventh base
=====================================
debian/tests/data/test.ref
=====================================
@@ -0,0 +1,2 @@
+>ref
+ATCGGCTAAAA
=====================================
debian/tests/data/test.ref.fai
=====================================
@@ -0,0 +1 @@
+ref 11 5 11 12
=====================================
debian/tests/data/test.vcf
=====================================
@@ -0,0 +1,14 @@
+##fileformat=VCFv4.1
+##INFO=<ID=NAME,Number=0,Type=String,Description="Test name">
+#CHROM POS ID REF ALT QUAL FILTER INFO
+ref 1 . A G 1234 PASS NAME=first base
+ref 2 . T . 1234 PASS NAME=second base
+ref 3 . C T 1234 PASS NAME=third base
+ref 4 . G A 1234 PASS NAME=fourth base
+ref 5 . G . 1234 PASS NAME=fifth base
+ref 6 . C G 1234 PASS NAME=sixth base
+ref 7 . T . 1234 PASS NAME=seventh base
+ref 8 . A T 1234 PASS NAME=eighth base
+ref 9 . A . 1234 PASS NAME=ninth base
+ref 10 . A . 1234 PASS NAME=tenth base
+ref 11 . A C 1234 PASS NAME=eleventh base
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,153 @@
+#!/bin/bash
+set -e
+
+pkg=freebayes
+
+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}"
+
+#do_stuff_to_test_package#
+ls -R
+
+echo -e "\e[93m\e[1mTest 1\e[0m"
+freebayes --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --ploidy 1 -f test.ref test.bam -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 2\e[0m"
+freebayes --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --ploidy 1 -f test.ref test.bam --region ref -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 3\e[0m"
+freebayes --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --ploidy 1 -f test.ref test.bam --region ref:4-5 --region ref:6-7 -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 4\e[0m"
+freebayes --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --ploidy 1 -f test.ref test.bam --region ref:4 --region ref:6 -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 5\e[0m"
+freebayes --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --ploidy 1 -f test.ref test.bam --targets test.bed -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 6\e[0m"
+freebayes --haplotype-length 0 --min-alternate-count 1 --min-alternate-fraction 0 --pooled-continuous --ploidy 1 -f test.ref test.bam --region ref:1,0-1,1 -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 7\e[0m"
+freebayes -f tiny/q.fa tiny/NA12878.chr22.tiny.bam -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 8\e[0m"
+for region in q:180-191 q:1002-1013 q:3250-3268 q:5003-5014 q:5632-5646 q:6412-6423 q:8840-8851 q:10526-10537 q:12119-12130;
+do
+ freebayes -f tiny/q.fa -F 0.2 tiny/NA12878.chr22.tiny.bam -r $region -v test.vcf
+done
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 9\e[0m"
+freebayes -f tiny/q.fa -F 0.2 tiny/NA12878.chr22.tiny.bam -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 10\e[0m"
+freebayes -f tiny/q.fa -F 0.2 tiny/NA12878.chr22.tiny.bam -t targets.bed -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 11\e[0m"
+freebayes -f tiny/q.fa tiny/NA12878.chr22.tiny.bam -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 12\e[0m"
+freebayes -f tiny/q.fa -l@ tiny/q.vcf.gz tiny/NA12878.chr22.tiny.bam -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 13\e[0m"
+freebayes -f tiny/q.fa -@ tiny/q_spiked.vcf.gz tiny/NA12878.chr22.tiny.bam -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 14\e[0m"
+freebayes -f tiny/q.fa -@ tiny/q_spiked.vcf.gz tiny/NA12878.chr22.tiny.bam -l -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 15\e[0m"
+freebayes -f tiny/q.fa -@ tiny/q.vcf.gz -l tiny/1read.bam -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 16\e[0m"
+freebayes -f tiny/q.fa -@ tiny/q_spiked.vcf.gz -r q:1-10000 tiny/NA12878.chr22.tiny.bam -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 17\e[0m"
+freebayes -f tiny/q.fa -@ tiny/q_spiked.vcf.gz -r q:1-10000 tiny/NA12878.chr22.tiny.bam -l -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 18\e[0m"
+freebayes -f tiny/q.fa -@ tiny/q_spiked.vcf.gz --stdin < tiny/NA12878.chr22.tiny.bam -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 19\e[0m"
+freebayes -f tiny/q.fa -@ tiny/q_spiked.vcf.gz -l --stdin < tiny/NA12878.chr22.tiny.bam -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 20\e[0m"
+freebayes -f tiny/q.fa tiny/NA12878.chr22.tiny.bam -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 21\e[0m"
+freebayes -f 'tiny/q with spaces.fa' tiny/NA12878.chr22.tiny.bam -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 22\e[0m"
+freebayes -f tiny/hla.fa -@ tiny/hla.vcf.gz -r HLA-DRB1*16:02:01:1-10000 tiny/NA12878.chr22.tiny.hla.bam -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 23\e[0m"
+freebayes -f splice/1:883884-887618.fa splice/1:883884-887618.bam -F 0.05 -C 1 -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 24\e[0m"
+freebayes -f tiny/q.fa -F 0.2 tiny/NA12878.chr22.tiny.bam --gvcf -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 25\e[0m"
+freebayes -f tiny/q.fa -F 0.2 tiny/NA12878.chr22.tiny.bam --gvcf --gvcf-chunk 50 -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 26\e[0m"
+freebayes -f tiny/q.fa -F 0.2 tiny/NA12878.chr22.tiny.bam --gvcf --gvcf-dont-use-chunk true -v test.vcf
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
View it on GitLab: https://salsa.debian.org/med-team/freebayes/-/compare/b70d4a06555e63566c0c11e3a24116834a771d2f...b133321160e087685ad170e46e497566d5c58620
--
View it on GitLab: https://salsa.debian.org/med-team/freebayes/-/compare/b70d4a06555e63566c0c11e3a24116834a771d2f...b133321160e087685ad170e46e497566d5c58620
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