work on examples

Author: brentp

src/main.rs

@@ -64,6 +64,14 @@ struct Args {
         default_value = "1"
     )]
     a_requirements: OverlapAmount,
+
+    #[arg(
+        help = "b-requirements for overlap. A float value < 1 or a number ending with % will be the fraction (or %) of the interval. An integer will be the number of bases.",
+        short = 'R',
+        long = "b-requirements",
+        default_value = "1"
+    )]
+    b_requirements: OverlapAmount,
 }
 
 #[global_allocator]
@@ -137,6 +145,7 @@ pub fn main() -> Result<(), Box<dyn std::error::Error>> {
             .a_part(args.a_part)
             .b_part(args.b_part)
             .a_requirements(args.a_requirements)
+            .b_requirements(args.b_requirements)
             .build(),
     );
     log::info!("report_options: {:?}", report_options);

src/writer.rs

@@ -133,6 +133,7 @@ impl Writer {
             Some(f) => f,
             None => unimplemented!("format must be specified"),
         };
+        let path = if path == "-" { "/dev/stdout" } else { path };
 
         // Use default compression if not specified
         let compression = compression.unwrap_or(Compression::None);

tests/examples/README.md

@@ -0,0 +1,90 @@
+Here we show examples of how `bedder` can perform intersections. All examples uses these files:
+
+#### aa.bed
+
+```
+chr1 2 23
+```
+
+#### bb.bed
+
+```
+chr1 8 12
+chr1 14 15
+chr1 20 30
+```
+
+# Reporting Part
+
+For, now, we focus on which part of each interval that is reported. The options for this are:
+
+```
+  -p, --a-part <A_PART>
+          a-part [default: whole] [possible values: none, part, whole, inverse]
+      --b-part <B_PART>
+          b-part [default: whole] [possible values: none, part, whole, inverse]
+```
+
+Let's start with reporting the *whole* `a` interval if it overlaps and *none* of the `b` interval:
+
+```
+$ bedder -a tests/examples/aa.bed -b tests/examples/bb.bed -g tests/examples/fake.fai --a-part whole --b-part none
+chr1    2       23
+```
+
+Now, we report the *part*s of the `a` interval along with the *whole* `b` interval that it overlapped:
+
+```
+$ bedder -a tests/examples/aa.bed -b tests/examples/bb.bed -g tests/examples/fake.fai --a-part part --b-part whole
+chr1    8       12      chr1    8       12
+chr1    14      15      chr1    14      15
+chr1    20      23      chr1    20      30
+```
+
+And now the *part* of `a` and the `part` of `b`:
+
+```
+$ bedder -a tests/examples/aa.bed -b tests/examples/bb.bed -g tests/examples/fake.fai --a-part part --b-part part
+chr1    8       12      chr1    8       12
+chr1    14      15      chr1    14      15
+chr1    20      23      chr1    20      23
+```
+
+We can also report the `inverse` that is, parts of `a` that do not overlap `b`:
+
+```
+$ bedder -a tests/examples/aa.bed -b tests/examples/bb.bed -g tests/examples/fake.fai --a-part inverse --b-part none
+chr1    2       8
+chr1    12      14
+chr1    15      20
+```
+
+There are other combinations of parameters, some of which are not very helpful!
+
+# Overlap Requirements
+
+The default in bedder is that a single base of overlap is sufficient to report. However we can add constraints to this with these arguments:
+
+```
+  -r, --a-requirements <A_REQUIREMENTS>
+          a-requirements for overlap. A float value < 1 or a number ending with % will be the fraction (or %) of the interval. An integer will be the number of bases. [default: 1]
+  -R, --b-requirements <B_REQUIREMENTS>
+          b-requirements for overlap. A float value < 1 or a number ending with % will be the fraction (or %) of the interval. An integer will be the number of bases. [default: 1]
+```
+
+Here is the default, requiring a single base of overlap:
+
+```
+$ bedder -a tests/examples/aa.bed -b tests/examples/bb.bed -g tests/examples/fake.fai --a-part part --b-part none --a-requirements 1
+chr1    8       12
+chr1    14      15
+chr1    20      23
+```
+
+We can update that to require at least 3 bases:
+
+```
+$ bedder -a tests/examples/aa.bed -b tests/examples/bb.bed -g tests/examples/fake.fai --a-part whole --b-part whole --a-requirements 3 --a-mode piece
+chr1    2       23      chr1    8       12      chr1    20      30
+chr1    2       23      chr1    8       12      chr1    20      30 # bug: TODO: printing this line twice
+```

tests/examples/fake.fai

@@ -0,0 +1 @@
+chr1	10000	10000