[Debian-med-packaging] Bug#905645: picard-tools: autopkgtest regression: Option 'ALIGNMENT_STATUS' is required.

[Paul Gevers]

Source: picard-tools
Version: 2.18.2+dfsg-1
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: regression

Dear maintainer(s),

Since the upload of version 2.18.2+dfsg-1 the autopkgtest of your
package started to fail. I have copied the output below.

Could you please investigate? It seems like the new version requires an
option that used to be absent or optional. Currently this failure is
contributing to delaying migration to testing with 13 days.

Note: maybe you want to "set -x" in your script for easier debug where
the script actually fails.

Paul

https://ci.debian.net/data/autopkgtest/testing/amd64/p/picard-tools/782819/log.gz


autopkgtest [09:11:52]: test run-unit-test: [-----------------------
ERROR: Option 'ALIGNMENT_STATUS' is required.

USAGE: ViewSam [options]

Documentation:
http://broadinstitute.github.io/picard/command-line-overview.html#ViewSam

Very simple command that just reads a SAM or BAM file andwrites out the
header and each record to standard out. When an
(optional) intervalsfile is specified, only records overlapping those
intervals will be output.
All reads, just the aligned reads, or just the unaligned reads can be
printed out bysetting AlignmentStatus accordingly.
The SAM or BAM header can be printed out separatelyusing HEADER_ONLY.
Only the alignment records can be printed using
RECORDS_ONLY.However, HEADER_ONLY and RECORDS_ONLY cannot both be
specified at one time.

Usage example:

java -jar picard.jar ViewSam
I=sample.bam
HEADER_ONLY=true

Version: 2.18.2


Options:

--help
-h                            Displays options specific to this tool.

--stdhelp
-H                            Displays options specific to this tool AND
options common to all Picard command line
                              tools.

--version                     Displays program version.

INPUT=String
I=String                      The SAM or BAM file or GA4GH url to view.
Required.

ALIGNMENT_STATUS=AlignmentStatus
                              Print out all reads, just the aligned
reads or just the unaligned reads.  Required.
                              Possible values: {Aligned, Unaligned, All}

PF_STATUS=PfStatus            Print out all reads, just the PF reads or
just the non-PF reads.  Required. Possible
                              values: {PF, NonPF, All}

HEADER_ONLY=Boolean           Print the SAM header only.  Default value:
false. This option can be set to 'null' to
                              clear the default value. Possible values:
{true, false}

RECORDS_ONLY=Boolean          Print the alignment records only.  Default
value: false. This option can be set to 'null'
                              to clear the default value. Possible
values: {true, false}

INTERVAL_LIST=File            An intervals file used to restrict what
records are output.  Default value: null.

autopkgtest [09:11:55]: test run-unit-test: -----------------------]

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