CollectAlignmentSummaryMetrics throws exception upon an empty BAM file (header only)

[nh13]

CollectAlignmentSummaryMetrics throws an exception when the input has no reads (SAM header only). CollectAlignmentSummaryMetrics is running as part of CollectMutipleMetrics, with the latter always producing a PDF output. Nonetheless, CollectAlignmentSummaryMetrics on an empty BAM file does not produce a histogram in the resulting metrics file, which causes the R script to fail.

ERROR	2022-11-28 13:33:21	ProcessExecutor	Error in read.table(metricsFile, header = T, sep = "\t", skip = secondBlankLine) : 
ERROR	2022-11-28 13:33:21	ProcessExecutor	  no lines available in input
ERROR	2022-11-28 13:33:21	ProcessExecutor	Execution halted
[Mon Nov 28 13:33:21 MST 2022] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=514850816
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" picard.PicardException: R script picard/analysis/readLengthDistribution.R failed with return code 1
	at picard.analysis.CollectAlignmentSummaryMetrics.finish(CollectAlignmentSummaryMetrics.java:199)
	at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:177)
	at picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:94)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
	at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)

[nh13]

For reference, other tools handle this a bit more gracefully:

WARNING	2022-11-28 13:40:01	QualityScoreDistribution	No valid bases found in input file. No plot will be produced.
WARNING	2022-11-28 13:40:01	MeanQualityByCycle	No valid bases found in input file. No plot will be produced.
WARNING	2022-11-28 13:40:01	CollectBaseDistributionByCycle	No valid bases found in input file. No plot will be produced.
INFO	2022-11-28 13:40:01	RExecutor	Executing R script via command: Rscript /var/folders/wh/hhg8fhpn2w52nxcnjjn548_c0000gn/T/script5121851671603744911.R <redacted>.gc_bias.detail_metrics.txt <redacted>.gc_bias.summary_metrics.txt <redacted>.gc_bias.pdf 100
ERROR	2022-11-28 13:40:02	ProcessExecutor	Error in read.table(summaryMetricsFile, header = T, sep = "\t", skip = firstBlankLine2) : 
ERROR	2022-11-28 13:40:02	ProcessExecutor	  no lines available in input
ERROR	2022-11-28 13:40:02	ProcessExecutor	Execution halted
WARNING	2022-11-28 13:40:02	CollectInsertSizeMetrics	All data categories were discarded because they contained < 0.05 of the total aligned paired data.
WARNING	2022-11-28 13:40:02	CollectInsertSizeMetrics	Total mapped pairs in all categories: 0.0

[kachulis]

Just noticed, this was fixed in #1859