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