From e1d6aad51764baf0cbc415df5d57e16584d1161e Mon Sep 17 00:00:00 2001 From: Nicole Rockweiler Date: Mon, 12 Jun 2023 14:50:42 -0400 Subject: [PATCH] Fix #1081. Make --USE_SEQUENTIAL_FASTQS help message more user friendly in FastqToSam.java - Issue #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). --- src/main/java/picard/sam/FastqToSam.java | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/main/java/picard/sam/FastqToSam.java b/src/main/java/picard/sam/FastqToSam.java index 402f43e8b5..2a74e2b91b 100644 --- a/src/main/java/picard/sam/FastqToSam.java +++ b/src/main/java/picard/sam/FastqToSam.java @@ -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; - @Argument(doc="Use sequential fastq files with the suffix _###.fastq or _###.fastq.gz." + - "The files should be named:\n" + + @Argument(doc="Use sequential fastq files with the suffix _###.fastq[.qz]." + + " The files should be named:\n" + " _001., _002., ..., _XYZ.\n" + - " The base files should be:\n" + - " _001.\n" + - " An example would be:\n" + + "Use the *first* file for the --FASTQ argument, e.g., --FASTQ _001..\n" + + "If paired end, use the *first* read2 file for the --FASTQ2 argument, e.g., _001..\n" + + "Example: combine and convert 4 single end fastqs with filenames:\n" + " RUNNAME_S8_L005_R1_001.fastq\n" + " RUNNAME_S8_L005_R1_002.fastq\n" + " RUNNAME_S8_L005_R1_003.fastq\n" + " RUNNAME_S8_L005_R1_004.fastq\n" + - "RUNNAME_S8_L005_R1_001.fastq should be provided as FASTQ.", optional=true) + "Run command with --FASTQ RUNNAME_S8_L005_R1_001.fastq --USE_SEQUENTIAL_FASTQS true", optional=true) public boolean USE_SEQUENTIAL_FASTQS = false; @Argument(shortName="V", doc="A value describing how the quality values are encoded in the input FASTQ file. " +