From 4d05a1ff9d6259379ca1a0fbf6f8600f888c5425 Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Mon, 21 Aug 2023 22:19:17 -0700 Subject: [PATCH] Apply suggestions from code review Co-authored-by: Tim Fennell --- docs/tools/AggregateSvPileup.md | 2 +- .../com/fulcrumgenomics/sv/tools/AggregateSvPileup.scala | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/tools/AggregateSvPileup.md b/docs/tools/AggregateSvPileup.md index 3fe95d0..55e9943 100644 --- a/docs/tools/AggregateSvPileup.md +++ b/docs/tools/AggregateSvPileup.md @@ -29,7 +29,7 @@ by the count of the union of templates that cross any constituent breakends. In straddle a breakend are considered to cross the breakend. If a BED file of target regions is provided, each aggregated pileup is annotated with whether its left and -right sides overlap a target region. Additionally, the names of the overlapping target regions will be copied +right sides overlap a target region. Additionally, the names of the overlapping target regions will be annotated, overwriting any values from the `SvPileup` input. If no target regions are provided, then the names of the overlapping target regions are copied from the `SvPiluep` input (if present). diff --git a/src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileup.scala b/src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileup.scala index ba8f94b..e55e272 100644 --- a/src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileup.scala +++ b/src/main/scala/com/fulcrumgenomics/sv/tools/AggregateSvPileup.scala @@ -11,7 +11,7 @@ import com.fulcrumgenomics.sv.{BreakpointPileup, Intervals} import com.fulcrumgenomics.util.{Io, Metric} import htsjdk.samtools.util.{Interval, OverlapDetector} import htsjdk.tribble.bed.BEDFeature -import com.fulcrumgenomics.FgBioDef.javaIterableToIterator +import com.fulcrumgenomics.FgBioDef._ import scala.collection.mutable @@ -39,7 +39,7 @@ import scala.collection.mutable |straddle a breakend are considered to cross the breakend. | |If a BED file of target regions is provided, each aggregated pileup is annotated with whether its left and - |right sides overlap a target region. Additionally, the names of the overlapping target regions will be copied + |right sides overlap a target region. Additionally, the names of the overlapping target regions will be |annotated, overwriting any values from the `SvPileup` input. If no target regions are provided, then the names |of the overlapping target regions are copied from the `SvPiluep` input (if present). | @@ -249,8 +249,8 @@ object BreakpointCategory extends Enumeration { * @param right_templates The total number of templates used for the denominator when calculating `right_frequency`. * @param left_overlaps_target True if the left aggregated region overlaps a target region * @param right_overlaps_target True if the right aggregated region overlaps a target region - * @param left_targets the comma-delimited list of target names overlapping the left breakpoint - * @param right_targets the comma-delimited list of target names overlapping the right breakpoint + * @param left_targets the comma-delimited list of target names overlapping the left breakpoint + * @param right_targets the comma-delimited list of target names overlapping the right breakpoint */ case class AggregatedBreakpointPileup(id: String, category: BreakpointCategory,