Merge branch 'main' into JD-24-pileup-circular

fulcrumgenomics · Sep 29, 2023 · 5aea888 · 5aea888
2 parents b755730 + f55b599
commit 5aea888
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Showing 3 changed files with 3 additions and 2 deletions.
diff --git 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
@@ -5,6 +5,7 @@ title: fgsv tools
 # fgsv tools
 
 The following tools are available in fgsv version 0.0.3-4fee506.
+
 ## 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
@@ -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 " +