Merge branch 'ar/gh-31-32' into 'master'

QOL fixes for pileup, fix duplex sampling bug

See merge request machine-learning/modkit!65

Author: ArtRand

CHANGELOG.md

@@ -3,6 +3,12 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## [v0.1.10]
+### Fixes
+- Don't log message whilst aggregating base modification probabilities (exposed with duplex reads as input).
+### Changes
+- [pileup] Fail fast when bam index doesn't contain any mapped reads.
+
 
 ## [v0.1.9]
 ### Changes

src/extract_mods.rs

@@ -21,8 +21,9 @@ use crate::position_filter::StrandedPositionFilter;
 use crate::read_ids_to_base_mod_probs::{
     ModProfile, ReadBaseModProfile, ReadsBaseModProfile,
 };
-use crate::reads_sampler::record_sampler::{RecordSampler, SamplingSchedule};
+use crate::reads_sampler::record_sampler::RecordSampler;
 use crate::reads_sampler::sample_reads_from_interval;
+use crate::reads_sampler::sampling_schedule::SamplingSchedule;
 use crate::record_processor::WithRecords;
 use crate::util::{
     get_master_progress_bar, get_spinner, get_subroutine_progress_bar,

src/pileup/subcommand.rs

@@ -17,6 +17,7 @@ use crate::writers::{
 };
 use anyhow::{anyhow, bail, Context};
 
+use crate::reads_sampler::sampling_schedule::IdxStats;
 use clap::{Args, ValueEnum};
 use crossbeam_channel::bounded;
 use indicatif::{MultiProgress, ParallelProgressIterator};
@@ -320,6 +321,22 @@ impl ModBamPileup {
                 )
             })
             .transpose()?;
+        // use the path here instead of passing the reader directly to avoid potentially
+        // changing mutable internal state of the reader.
+        IdxStats::new_from_path(
+            &self.in_bam,
+            region.as_ref(),
+            position_filter.as_ref(),
+        )
+        .and_then(|index_stats| {
+            if index_stats.mapped_read_count > 0 {
+                Ok(())
+            } else {
+                Err(anyhow!("did not find any mapped reads, perform alignment first or use \
+                modkit extract and/or modkit summary to inspect unaligned modBAMs"))
+            }
+        })?;
+
         if self.filter_percentile > 1.0 {
             bail!("filter percentile must be <= 1.0")
         }

src/read_ids_to_base_mod_probs.rs

@@ -50,19 +50,12 @@ impl ReadIdsToBaseModProbs {
         canonical_base: DnaBase,
         mod_probs: Vec<BaseModProbs>,
     ) {
-        let added = self
-            .inner
+        self.inner
             .entry(read_id.to_owned())
             .or_insert(HashMap::new())
-            .insert(canonical_base, mod_probs);
-        if added.is_some() {
-            debug!(
-                "double added base mod calls for base {} and read {},\
-                 potentially a logic error, please submit an issue.",
-                canonical_base.char(),
-                read_id
-            );
-        }
+            .entry(canonical_base)
+            .or_insert(Vec::new())
+            .extend(mod_probs)
     }
 
     #[inline]
@@ -270,6 +263,9 @@ impl RecordProcessor for ReadIdsToBaseModProbs {
                                 &record,
                             );
 
+                        // must stay such that mod_probs will not be empty if seq_pos_base_mod_probs
+                        // is Some otherwise added_mod_probs_for_record should not be flipped to
+                        // true
                         if let Some(seq_pos_base_mod_probs) =
                             seq_pos_base_mod_probs
                         {
@@ -289,7 +285,7 @@ impl RecordProcessor for ReadIdsToBaseModProbs {
                                 canonical_base,
                                 mod_probs,
                             );
-                            added_probs_for_record = true
+                            added_probs_for_record = true;
                         } else {
                             // trace!("all base mod positions were removed by filtering \
                             //     for {record_name} and base {raw_canonical_base}");

src/reads_sampler/mod.rs

@@ -1,10 +1,11 @@
 pub(crate) mod record_sampler;
+pub(crate) mod sampling_schedule;
 
 use crate::interval_chunks::IntervalChunks;
 use crate::mod_bam::{CollapseMethod, EdgeFilter};
 use crate::monoid::Moniod;
 use crate::position_filter::StrandedPositionFilter;
-use crate::reads_sampler::record_sampler::SamplingSchedule;
+use crate::reads_sampler::sampling_schedule::SamplingSchedule;
 use crate::record_processor::{RecordProcessor, WithRecords};
 use crate::util::{
     get_master_progress_bar, get_subroutine_progress_bar, get_targets,