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 <[email protected]> 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@WZ6VQMQ?9Y?L7ORM6BF=QBGJXBNCLENRXCRJZXN9@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@9NXZJRCXRNELCNBXJGBQ=FB6MRO7L?Y9?QMQV6ZW@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@WZ6VQMQ?9Y?L7ORM6BF=QBGJXBNCLENRXCRJZXN9@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@9NXZJRCXRNELCNBXJGBQ=FB6MRO7L?Y9?QMQV6ZW@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@WZ6VQMQ?9Y?L7ORM6BF=QBGJXBNCLENRXCRJZXN9@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@9NXZJRCXRNELCNBXJGBQ=FB6MRO7L?Y9?QMQV6ZW@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.
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