enh: filter_read also takes Option<&Alignment>

examples/par_granges_example.rs

@@ -5,7 +5,7 @@ use perbase_lib::{
     position::pileup_position::PileupPosition,
     read_filter::ReadFilter,
 };
-use rust_htslib::bam::{self, record::Record, Read};
+use rust_htslib::bam::{self, pileup::Alignment, record::Record, Read};
 use std::path::PathBuf;
 
 // To use ParGranges you will need to implement a [`RegionProcessor`](par_granges::RegionProcessor),
@@ -32,7 +32,7 @@ struct BasicReadFilter {
 impl ReadFilter for BasicReadFilter {
     // Filter reads based SAM flags and mapping quality, true means pass
     #[inline]
-    fn filter_read(&self, read: &Record) -> bool {
+    fn filter_read(&self, read: &Record, _alignment: Option<&Alignment>) -> bool {
         let flags = read.flags();
         (!flags) & &self.include_flags == 0
             && flags & &self.exclude_flags == 0

src/commands/only_depth.rs

@@ -307,7 +307,7 @@ impl<F: ReadFilter> OnlyDepthProcessor<F> {
         for record in reader
             .rc_records()
             .map(|r| r.expect("Read record"))
-            .filter(|read| self.read_filter.filter_read(&read))
+            .filter(|read| self.read_filter.filter_read(&read, None))
             .flat_map(|record| IterAlignedBlocks::new(record, self.mate_fix))
         {
             let rec_start = u32::try_from(record.0).expect("check overflow");
@@ -396,7 +396,7 @@ impl<F: ReadFilter> OnlyDepthProcessor<F> {
         for record in reader
             .rc_records()
             .map(|r| r.expect("Read record"))
-            .filter(|read| self.read_filter.filter_read(&read))
+            .filter(|read| self.read_filter.filter_read(&read, None))
         {
             let rec_start = u32::try_from(record.reference_start()).expect("check overflow");
             let rec_stop = u32::try_from(record.reference_end()).expect("check overflow");

src/lib/mod.rs

@@ -17,7 +17,7 @@
 //!     position::pileup_position::PileupPosition,
 //!     read_filter::ReadFilter,
 //! };
-//! use rust_htslib::bam::{self, record::Record, Read};
+//! use rust_htslib::bam::{self, record::Record, Read, pileup::Alignment};
 //! use std::path::PathBuf;
 //!
 //! // To use ParGranges you will need to implement a [`RegionProcessor`](par_granges::RegionProcessor),
@@ -44,7 +44,7 @@
 //! impl ReadFilter for BasicReadFilter {
 //!     // Filter reads based SAM flags and mapping quality, true means pass
 //!     #[inline]
-//!     fn filter_read(&self, read: &Record) -> bool {
+//!     fn filter_read(&self, read: &Record, _: Option<&Alignment>) -> bool {
 //!         let flags = read.flags();
 //!         (!flags) & &self.include_flags == 0
 //!             && flags & &self.exclude_flags == 0

src/lib/position/pileup_position.rs

@@ -72,7 +72,7 @@ impl PileupPosition {
         read_filter: &F,
         base_filter: Option<u8>,
     ) {
-        if !read_filter.filter_read(&record) {
+        if !read_filter.filter_read(&record, Some(alignment)) {
             self.depth -= 1;
             self.fail += 1;
             return;
@@ -201,9 +201,10 @@ impl PileupPosition {
                     Ordering::Less => Ordering::Less,
                     Ordering::Equal => {
                         // Check if a is first in pair
-                        if a.1.flags() & 64 == 0 && read_filter.filter_read(&a.1) {
+                        if a.1.flags() & 64 == 0 && read_filter.filter_read(&a.1, Some(&a.0)) {
                             Ordering::Greater
-                        } else if b.1.flags() & 64 == 0 && read_filter.filter_read(&b.1) {
+                        } else if b.1.flags() & 64 == 0 && read_filter.filter_read(&b.1, Some(&b.0))
+                        {
                             Ordering::Less
                         } else {
                             // Default to `a` in the event that there is no first in pair for some reason

src/lib/read_filter.rs

@@ -1,10 +1,11 @@
 //! A trait and default implementation of a read filter.
+use rust_htslib::bam::pileup::Alignment;
 use rust_htslib::bam::record::Record;
 
 /// Anything that implements ReadFilter can apply a filter set to read.
 pub trait ReadFilter {
     /// filters a read, true is pass, false if fail
-    fn filter_read(&self, read: &Record) -> bool;
+    fn filter_read(&self, read: &Record, alignment: Option<&Alignment>) -> bool;
 }
 
 /// A straightforward read filter.
@@ -28,7 +29,7 @@ impl DefaultReadFilter {
 impl ReadFilter for DefaultReadFilter {
     /// Filter reads based SAM flags and mapping quality
     #[inline(always)]
-    fn filter_read(&self, read: &Record) -> bool {
+    fn filter_read(&self, read: &Record, _alignment: Option<&Alignment>) -> bool {
         let flags = read.flags();
         (!flags) & &self.include_flags == 0
             && flags & &self.exclude_flags == 0