[med-svn] [Git][med-team/bio-vcf][master] 3 commits: Add autopkgtests

Thu Jan 28 15:52:25 GMT 2021


Nilesh Patra pushed to branch master at Debian Med / bio-vcf


Commits:
c2994adc by Nilesh Patra at 2021-01-28T21:18:55+05:30
Add autopkgtests

- - - - -
ae935608 by Nilesh Patra at 2021-01-28T21:19:26+05:30
Add "Rules-Requires-Root:no"

- - - - -
b77acb06 by Nilesh Patra at 2021-01-28T15:51:24+00:00
Add manpages

- - - - -


5 changed files:

- + debian/bio-vcf.1
- debian/control
- + debian/createmanpages
- + debian/tests/control
- + debian/tests/run-unit-test


Changes:

=====================================
debian/bio-vcf.1
=====================================
@@ -0,0 +1,110 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
+.TH BIO-VCF "1" "January 2021" "bio-vcf 0.9.5" "User Commands"
+.SH NAME
+bio-vcf \- domain specific language (DSL) for processing the VCF format
+.SH SYNOPSIS
+.B bio-vcf
+[\fI\,options\/\fR] \fI\,filename\/\fR
+.SH DESCRIPTION
+\fI\,/usr/lib/ruby/vendor_ruby/rubygems/defaults/operating_system\/\fP.rb:10: warning: constant Gem::ConfigMap is deprecated
+bio\-vcf 0.9.5 (biogem Ruby 2.7.1 with pcows) by Pjotr Prins 2015\-2020
+.PP
+e.g.  bio\-vcf < test/data/input/somaticsniper.vcf
+.TP
+\fB\-i\fR, \fB\-\-ignore\-missing\fR
+Ignore missing data
+.TP
+\fB\-\-filter\fR cmd
+Evaluate filter on each record
+.TP
+\fB\-\-sfilter\fR cmd
+Evaluate filter on each sample
+.TP
+\fB\-\-sfilter\-samples\fR list
+Filter on selected samples (e.g., 0,1
+.TP
+\fB\-\-ifilter\fR, \fB\-\-if\fR cmd
+Include filter
+.TP
+\fB\-\-ifilter\-samples\fR list
+Include set \- implicitely defines exclude set
+.TP
+\fB\-\-efilter\fR, \fB\-\-ef\fR cmd
+Exclude filter
+.TP
+\fB\-\-efilter\-samples\fR list
+Exclude set \- overrides exclude set
+.TP
+\fB\-\-add\-filter\fR name
+Set/add filter field to name
+.TP
+\fB\-\-bed\fR bedfile
+Filter on BED elements
+.TP
+\fB\-e\fR, \fB\-\-eval\fR cmd
+Evaluate command on each record
+.TP
+\fB\-\-eval\-once\fR cmd
+Evaluate command once (usually for header info)
+.TP
+\fB\-\-seval\fR cmd
+Evaluate command on each sample
+.TP
+\fB\-\-rewrite\fR eval
+Rewrite INFO
+.TP
+\fB\-\-samples\fR list
+Output selected samples
+.TP
+\fB\-\-rdf\fR
+Generate Turtle RDF (also check out \fB\-\-template\fR!)
+.TP
+\fB\-\-num\-threads\fR [num]
+Multi\-core version (default ALL)
+.TP
+\fB\-\-thread\-lines\fR num
+Fork thread on num lines (default 40000)
+.TP
+\fB\-\-skip\-header\fR
+Do not output VCF header info
+.TP
+\fB\-\-set\-header\fR list
+Set a special tab delimited output header (#samples expands to sample names)
+.TP
+\fB\-t\fR, \fB\-\-template\fR erb
+Use ERB template for output
+.TP
+\fB\-\-add\-header\-tag\fR
+Add bio\-vcf status tag to header output
+.TP
+\fB\-\-timeout\fR [num]
+Timeout waiting for thread to complete (default 180)
+.TP
+\fB\-\-names\fR
+Output sample names
+.TP
+\fB\-\-statistics\fR
+Output statistics
+.TP
+\fB\-q\fR, \fB\-\-quiet\fR
+Run quietly
+.TP
+\fB\-v\fR, \fB\-\-verbose\fR
+Run verbosely
+.TP
+\fB\-\-debug\fR
+Show debug messages and keep intermediate output
+.TP
+\fB\-\-id\fR name
+Identifier
+.TP
+\fB\-\-tags\fR list
+Add tags
+.TP
+\fB\-h\fR, \fB\-\-help\fR
+display this help and exit
+.PP
+Vcf parser
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.


=====================================
debian/control
=====================================
@@ -11,6 +11,7 @@ Vcs-Browser: https://salsa.debian.org/med-team/bio-vcf
 Vcs-Git: https://salsa.debian.org/med-team/bio-vcf.git
 Homepage: https://rubygems.org/gems/bio-vcf/
 XS-Ruby-Versions: all
+Rules-Requires-Root: no
 
 Package: bio-vcf
 Architecture: all


=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,29 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr --help-option="-h" \
+         --name="$NAME" \
+            --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+    http://liw.fi/manpages/
+EOT
+


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


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,31 @@
+#!/bin/bash
+set -e
+
+CUR_DIR=`pwd`
+
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+  AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+  trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp -a ${CUR_DIR}/"test"/data/input/* $AUTOPKGTEST_TMP
+
+cd $AUTOPKGTEST_TMP
+gunzip -r *
+
+echo "Test 1"
+bio-vcf < somaticsniper.vcf 1> test1
+[ -s test1 ] || exit 1
+fgrep -q "TUMOR" test1
+rm -f ./test1
+echo "================================="
+echo "PASS"
+
+echo "Test 2"
+bio-vcf --rdf --skip-header --eval '[r.alt,r.info.dp,r.tumor.gq.to_s]' < multisample.vcf  > test2
+fgrep -q prefix test2 
+rm -f ./test2
+echo "=================================="
+echo "PASS"
+
+



View it on GitLab: https://salsa.debian.org/med-team/bio-vcf/-/compare/cd918a04ea4acffcea61e7fb9e23a465b5e0ab59...b77acb06bbc2fa69738ef2393b74a861ee99b5c7

-- 
View it on GitLab: https://salsa.debian.org/med-team/bio-vcf/-/compare/cd918a04ea4acffcea61e7fb9e23a465b5e0ab59...b77acb06bbc2fa69738ef2393b74a861ee99b5c7
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