GRangesEmpty added and major changes added. This newtype resolves man…

…y issues.

 - Added the GRangesEmpty newtype around `GRanges<R, ()>`. This was
   a major step forward. The reason for this type is that when the
   generic `GRanges<R, T>` object does not have a data container
   (i.e. `T = ()`, this *always* corresponds to the case where
   the range container `R` has ranges without indices. As such, working
   with the unwrapped "empty" `GRanges` object was a bit of a headache,
   since the developer would need to handle and link *two* types: `T = ()`
   and some sort of unindexed range. The newtype resolves this.

 - Added the `IntoGRangesRef` trait, which improves the ergonomics
   when writing functions that should work on both `GRanges` and `GRangesEmpty`
   objects. Also added `Into` methods for conversion from `GRangesEmpty` to
   `GRanges` objects.

 - With two different types now, it is possible to *properly*
   have the same method (without traits) for both `GRanges` and
   `GRangesEmpty` types. Thus, several methods like
   `from_iter_ranges_only()` and `push_range_with_data()` have been removed
   and replaced with unified method names `from_iter()` and `push_range`
   using the proper function for their type.

 - Added error for unsupported ranges format.

src/commands.rs

@@ -1,12 +1,12 @@
 use std::path::PathBuf;
 
 use crate::{
- granges::GRangesVariant,
  io::OutputFile,
  prelude::*,
  ranges::operations::adjust_range,
  reporting::{CommandOutput, Report},
  test_utilities::random_granges,
+ traits::{IterableRangeContainer, TsvSerialize},
  PositionOffset,
 };
 
@@ -69,44 +69,37 @@ pub fn granges_adjust(
 
  Ok(CommandOutput::new((), report))
 }
-
-/// Retain only the ranges that have at least one overlap with another set of ranges.
-pub fn granges_filter(
- seqlens: &PathBuf,
- left_bedfile: &PathBuf,
- right_bedfile: &PathBuf,
- output: Option<&PathBuf>,
- sort: bool,
-) -> Result<CommandOutput<()>, GRangesError> {
- let genome = read_seqlens(seqlens)?;
-
- // in memory (sorted queries not yet supported)
- let left_record_iter = BedlikeIterator::new(left_bedfile)?
- .into_variant()?;
- let right_record_iter = BedlikeIterator::new(right_bedfile)?
- .into_variant()?;
-
- let left_gr = GRanges::from_iter_variant(left_record_iter, &genome)?;
- let right_gr = GRanges::from_iter_variant(right_record_iter, &genome)?;
-
- todo!()
- //let right_gr = right_gr.to_coitrees();
-
- //let intersection = left_gr.filter_overlaps(&right_gr)?;
-
- //// output stream -- header is None for now (TODO)
- //let output_stream = output.map_or(OutputFile::new_stdout(None), |file| {
- // OutputFile::new(file, None)
- //});
- //let mut writer = output_stream.writer()?;
-
- //// for reporting stuff to the user
- //let mut report = Report::new();
-
- //intersection.sort().to_tsv(output)?;
-
- //Ok(CommandOutput::new((), report))
-}
+//
+// /// Retain only the ranges that have at least one overlap with another set of ranges.
+// pub fn granges_filter<DL, DR>(
+// seqlens: &PathBuf,
+// left_granges: GRanges<VecRangesEmpty, DL>,
+// right_granges: GRanges<VecRangesEmpty, DR>,
+// sort: bool,
+// ) -> Result<CommandOutput<()>, GRangesError>
+// where
+// // we must be able to iterate over left ranges
+// VecRangesEmpty: IterableRangeContainer, 
+// // we must be able to convert the right GRanges to interval trees
+// GRanges<VecRangesEmpty, ()>: GenomicRangesToIntervalTrees<()>,
+// {
+// let right_granges = right_granges.to_coitrees()?;
+//
+// // let intersection = left_granges.filter_overlaps_(&right_granges)?;
+//
+// //// output stream -- header is None for now (TODO)
+// //let output_stream = output.map_or(OutputFile::new_stdout(None), |file| {
+// // OutputFile::new(file, None)
+// //});
+// //let mut writer = output_stream.writer()?;
+//
+// // for reporting stuff to the user
+// let mut report = Report::new();
+//
+// //intersection.sort().to_tsv(output)?;
+//
+// Ok(CommandOutput::new((), report))
+// }
 
 /// Generate a random BED-like file with genomic ranges.
 pub fn granges_random_bed(

src/data/mod.rs

@@ -4,4 +4,5 @@ use crate::traits::DataContainer;
 
 pub mod vec;
 
-impl<U> DataContainer for Vec<U>{}
+impl<U> DataContainer for Vec<U> {}
+impl DataContainer for () {}

src/error.rs

@@ -42,4 +42,7 @@ pub enum GRangesError {
  #[error("Invalid GRanges object: no data container.")]
  NoDataContainer,
 
+ // Command line tool related errors
+ #[error("Unsupported genomic range format")]
+ UnsupportedGenomicRangesFileFormat,
 }