From f55b599b44041a388260e8d94c922233c476761e Mon Sep 17 00:00:00 2001 From: Tim Fennell Date: Fri, 29 Sep 2023 14:16:12 -0600 Subject: [PATCH] Fix to AggregateSvPileup's documentation of the --bam parameter. (#27) * Fix to AggregateSvPileup's documentation of the --bam parameter. --- docs/tools/AggregateSvPileup.md | 2 +- docs/tools/index.md | 2 +- .../scala/com/fulcrumgenomics/sv/tools/AggregateSvPileup.scala | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/tools/AggregateSvPileup.md b/docs/tools/AggregateSvPileup.md index 55e9943..bc37268 100644 --- a/docs/tools/AggregateSvPileup.md +++ b/docs/tools/AggregateSvPileup.md @@ -43,7 +43,7 @@ pileups in the cluster. |Name|Flag|Type|Description|Required?|Max Values|Default Value(s)| |----|----|----|-----------|---------|----------|----------------| |input|i|FilePath|Input text file of pileups generated by SvPileup|Required|1|| -|bam|b|PathToBam|Bam file for allele frequency analysis. Must be the same file that was used as input to SvPileup.|Optional|1|| +|bam|b|PathToBam|Bam file for allele frequency analysis. Must be coordinate sorted version of the file that was input to SvPileup.|Optional|1|| |flank|f|Int|If BAM file is provided: distance upstream and downstream of aggregated breakpoint regions to search for mapped templates that overlap breakends. These are the templates that will be partitioned into those supporting the breakpoint vs. reading through it for the allele frequency calculation. Recommended to use at least the max read pair inner distance used by SvPileup.|Optional|1|1000| |min-breakpoint-support||Int|If BAM file is provided: minimum total number of templates supporting an aggregated breakpoint to report allele frequency. Supports speed improvement by avoiding querying and iterating over huge read pileups that contain insufficient support for a breakpoint to be considered interesting.|Optional|1|10| |min-frequency||Double|If BAM file is provided: minimum allele frequency to report. Supports speed improvement by avoiding iterating over huge read pileups that contain insufficient support for a breakpoint to be considered interesting.|Optional|1|0.001| diff --git a/docs/tools/index.md b/docs/tools/index.md index be706a9..df8d734 100644 --- a/docs/tools/index.md +++ b/docs/tools/index.md @@ -4,7 +4,7 @@ title: fgsv tools # fgsv tools -The following tools are available in fgsv version 0.0.2-9cbf8a5. +The following tools are available in fgsv version 0.0.3-d6090a5. ## All tools All tools. diff --git a/src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileup.scala b/src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileup.scala index 28bd27e..ce0d61f 100644 --- a/src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileup.scala +++ b/src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileup.scala @@ -50,7 +50,7 @@ import scala.collection.mutable |""") class AggregateSvPileup (@arg(flag='i', doc="Input text file of pileups generated by SvPileup") input: FilePath, - @arg(flag='b', doc="Bam file for allele frequency analysis. Must be the same file that was used as input to SvPileup.") + @arg(flag='b', doc="Bam file for allele frequency analysis. Must be coordinate sorted version of the file that was input to SvPileup.") bam: Option[PathToBam] = None, @arg(flag='f', doc="If BAM file is provided: distance upstream and downstream of aggregated breakpoint regions to " + "search for mapped templates that overlap breakends. These are the templates that will be partitioned into those " +