FastqToSam now breaks with gzipped FASTQ input

[mjhipp]

Bug Report

After #1794, FastqToSam no longer works with gzipped input.

Affected tool(s)

• FastqToSam

Affected version(s)

• Latest public release version
• Latest development/master branch as of 5/25/2022
• d784ca3 and after

Not affected: 9eafe4e and before

Description

Steps to reproduce

Run FastqToSam with gzipped input.

❯ java -jar picard.jar FastqToSam \
   FASTQ= sample.R1.fastq.gz \
   FASTQ2= sample.R2.fastq.gz \
   SO=queryname \
   O= out.bam \
   SAMPLE_NAME=sample

If you unzip and run again with unzipped fastqs, it works as expected.

Expected behavior

Gzipped FASTQs should be converted to SAM/BAM as in previous versions.

Even after updates, the help string says that gzipped input is supported:

FASTQ=PicardHtsPath
F1=PicardHtsPath              Input fastq file (optionally gzipped) for single end data, or first read in paired end
                              data.  Required.

FASTQ2=PicardHtsPath
F2=PicardHtsPath              Input fastq file (optionally gzipped) for the second read of paired end data.  Default
                              value: null.

Actual behavior

Failure when creating/referencing the FastqReader.

[Wed May 25 13:32:52 PDT 2022] FastqToSam FASTQ=sample.R1.fastq.gz FASTQ2=sample.R2.fastq.gz OUTPUT=out.bam SAMPLE_NAME=sample SORT_ORDER=queryname    USE_SEQUENTIAL_FASTQS=false READ_GROUP_NAME=A MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Wed May 25 13:32:52 PDT 2022] Executing as *** on Mac OS X 10.16 x86_64; OpenJDK 64-Bit Server VM 1.8.0_292-b10; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.27.1-1-gd784ca3-SNAPSHOT
[Wed May 25 13:32:52 PDT 2022] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=257425408
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMException: Input length = 1 at line 1 in fastq
	at htsjdk.samtools.fastq.FastqReader.readNextRecord(FastqReader.java:139)
	at htsjdk.samtools.fastq.FastqReader.<init>(FastqReader.java:94)
	at picard.sam.FastqToSam.fileToFastqReader(FastqToSam.java:439)
	at picard.sam.FastqToSam.doWork(FastqToSam.java:328)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:306)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
	at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
Caused by: java.nio.charset.MalformedInputException: Input length = 1
	at java.nio.charset.CoderResult.throwException(CoderResult.java:281)
	at sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:339)
	at sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
	at java.io.InputStreamReader.read(InputStreamReader.java:184)
	at java.io.BufferedReader.fill(BufferedReader.java:161)
	at java.io.BufferedReader.readLine(BufferedReader.java:324)
	at java.io.BufferedReader.readLine(BufferedReader.java:389)
	at htsjdk.samtools.fastq.FastqReader.readLineConditionallySkippingBlanks(FastqReader.java:207)
	at htsjdk.samtools.fastq.FastqReader.readNextRecord(FastqReader.java:104)
	... 6 more

[cmnbroad]

Oh yeah, I see how this happened in #1794. I'll make a PR - it's an easy fix.