Fix #1081. Make --USE_SEQUENTIAL_FASTQS help message more user friendly #1891
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…re user friendly in FastqToSam.java - Issue broadinstitute#1081 raised that help message for FastqToSam.java's --USE_SEQUENTIAL_FASTQS was not very intuititive. - Updated help message with more explicit usage (specific text on how to use the option and example commands).
droazen
reviewed
Jun 13, 2023
| @@ -161,17 +161,17 @@ public class FastqToSam extends CommandLineProgram { | |||
| @Argument(shortName="F2", doc="Input fastq file (optionally gzipped) for the second read of paired end data.", optional=true) | |||
| public PicardHtsPath FASTQ2; | |||
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| @Argument(doc="Use sequential fastq files with the suffix <prefix>_###.fastq or <prefix>_###.fastq.gz." + | |||
| "The files should be named:\n" + | |||
| @Argument(doc="Use sequential fastq files with the suffix <prefix>_###.fastq[.qz]." + | |||
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This should be [.gz], not [.qz]
tmelman
suggested changes
Jun 13, 2023
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Issue How to use USE_SEQUENTIAL_FASTQS option #1081 raised that help message for FastqToSam.java's --USE_SEQUENTIAL_FASTQS was not very intuititive. When I used this tool for the first time today, I also found the documentation confusing. Therefore, I made a PR.
Updated help message with more explicit usage (specific text on how to use the option and example commands).
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