From 731ddea2cbb5efd723eb7c582c8e8a2d4220d0db Mon Sep 17 00:00:00 2001 From: Soo Hee Lee Date: Tue, 11 Jul 2017 16:48:50 -0400 Subject: [PATCH] update DownsampleSam doc to reflect required metrics file in example command and new piping in feature --- src/main/java/picard/sam/DownsampleSam.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/main/java/picard/sam/DownsampleSam.java b/src/main/java/picard/sam/DownsampleSam.java index 06b69d5c5..41822d511 100644 --- a/src/main/java/picard/sam/DownsampleSam.java +++ b/src/main/java/picard/sam/DownsampleSam.java @@ -73,10 +73,11 @@ "
" +
             "java -jar picard.jar DownsampleSam \\
" +
             "      I=input.bam \\
" +
+            "      METRICS_FILE=downsample_metrics.txt \\
" +
             "      O=downsampled.bam" +
             "
" + "
"; - @Option(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "The input SAM or BAM file to downsample.") + @Option(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "The input SAM or BAM file to downsample. Starting v2.9.5, supports piping from stdin") public File INPUT; @Option(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "The output, downsampled, SAM or BAM file to write.")