mereg dev into main

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "oarfish"
-version = "0.3.0"
+version = "0.3.1"
 edition = "2021"
 authors = [
   "Zahra Zare Jousheghani <[email protected]>",
@@ -34,9 +34,9 @@ anyhow = "1.0.80"
 bio-types = "1.0.1"
 clap = { version = "4.5.1", features = ["derive"] }
 coitrees = "0.4.0"
-noodles-bam = "0.55.0"
+noodles-bam = "0.56.0"
 noodles-gtf = "0.23.0"
-noodles-sam = "0.52.0"
+noodles-sam = "0.53.0"
 num-format = "0.4.4"
 tabled = "0.15.0"
 tracing = "0.1.40"

src/bootstrap.rs

@@ -1,52 +1,6 @@
 use rand::distributions::{Distribution, Uniform};
 use rand::Rng;
 
-/// Wraps an iterator `I` to produce a new iterator that samples the original
-/// with replacement.
-pub struct SampleWithReplaceIter<'b, I: ExactSizeIterator> {
-    pub inds: &'b [usize],
-    pub iter: I,
-    pub idx: usize,
-    pub e_ptr: usize,
-    pub prev: Option<I::Item>,
-}
-
-impl<'b, I: ExactSizeIterator> Iterator for SampleWithReplaceIter<'b, I>
-where
-    I::Item: Copy,
-{
-    type Item = I::Item;
-
-    #[inline]
-    fn next(&mut self) -> Option<Self::Item> {
-        if let Some(next_ind) = self.inds.get(self.idx) {
-            // always makes sure we have a previous
-            // element. This will get the first
-            // element but wont yet increment
-            // the pointer (e_ptr)
-            if self.prev.is_none() {
-                self.prev = self.iter.next();
-            }
-            // next element is not a duplicate
-            if self.e_ptr != *next_ind {
-                // otherwise, call next until we have the
-                // correct element
-                loop {
-                    self.prev = self.iter.next();
-                    self.e_ptr += 1;
-                    if self.e_ptr == *next_ind {
-                        break;
-                    }
-                }
-            }
-            self.idx += 1;
-            self.prev
-        } else {
-            None
-        }
-    }
-}
-
 pub fn get_sample_inds<R: Rng + ?Sized>(n: usize, rng: &mut R) -> Vec<usize> {
     let dist = Uniform::new(0, n);
     let mut inds: Vec<usize> = dist.sample_iter(rng).take(n).collect();

src/em.rs

@@ -237,13 +237,7 @@ pub fn do_bootstrap(em_info: &EMInfo) -> Vec<f64> {
 
     // function that produces an iterator over the
     // scored alignments on demand
-    let make_iter = || bootstrap::SampleWithReplaceIter {
-        inds: &inds,
-        iter: em_info.eq_map.iter(),
-        idx: 0,
-        e_ptr: 0,
-        prev: None,
-    };
+    let make_iter = || em_info.eq_map.random_sampling_iter(&inds);
 
     do_em(em_info, make_iter, false)
 }

src/main.rs

@@ -9,6 +9,8 @@ use std::{
 };
 
 use num_format::{Locale, ToFormattedString};
+use serde::Serialize;
+use serde_json::json;
 use tracing::info;
 use tracing_subscriber::{filter::LevelFilter, fmt, prelude::*, EnvFilter};
 
@@ -30,14 +32,14 @@ use crate::util::write_function::{write_infrep_file, write_output};
 /// These represent different "meta-options", specific settings
 /// for all of the different filters that should be applied in
 /// different cases.
-#[derive(Clone, Debug, clap::ValueEnum)]
+#[derive(Clone, Debug, clap::ValueEnum, Serialize)]
 enum FilterGroup {
     NoFilters,
     NanocountFilters,
 }
 
 /// accurate transcript quantification from long-read RNA-seq data
-#[derive(Parser, Debug)]
+#[derive(Parser, Debug, Serialize)]
 #[clap(author, version, about, long_about = None)]
 struct Args {
     /// be quiet (i.e. don't output log messages that aren't at least warnings)
@@ -168,6 +170,31 @@ fn get_filter_opts(args: &Args) -> AlignmentFilters {
     }
 }
 
+fn get_json_info(args: &Args, emi: &EMInfo) -> serde_json::Value {
+    let prob = if args.model_coverage {
+        "binomial"
+    } else {
+        "no_coverage"
+    };
+
+    json!({
+        "prob_model" : prob,
+        "num_bins" : args.bins,
+        "filter_options" : &emi.eq_map.filter_opts,
+        "discard_table" : &emi.eq_map.discard_table,
+        "alignments": &args.alignments,
+        "output": &args.output,
+        "verbose": &args.verbose,
+        "quiet": &args.quiet,
+        "em_max_iter": &args.max_em_iter,
+        "em_convergence_thresh": &args.convergence_thresh,
+        "threads": &args.threads,
+        "filter_group": &args.filter_group,
+        "short_quant": &args.short_quant,
+        "num_bootstraps": &args.num_bootstraps
+    })
+}
+
 fn main() -> anyhow::Result<()> {
     let env_filter = EnvFilter::builder()
         .with_default_directive(LevelFilter::INFO.into())
@@ -254,8 +281,8 @@ fn main() -> anyhow::Result<()> {
 
     // if we are seeding the quantification estimates with short read
     // abundances, then read those in here.
-    let init_abundances = args.short_quant.map(|sr_path| {
-        read_short_quant_vec(&sr_path, &txps_name).unwrap_or_else(|e| panic!("{}", e))
+    let init_abundances = args.short_quant.as_ref().map(|sr_path| {
+        read_short_quant_vec(sr_path, &txps_name).unwrap_or_else(|e| panic!("{}", e))
     });
 
     // wrap up all of the relevant information we need for estimation
@@ -274,16 +301,12 @@ fn main() -> anyhow::Result<()> {
         em::em(&emi, args.threads)
     };
 
+    // prepare the JSON object we'll write
+    // to meta_info.json
+    let json_info = get_json_info(&args, &emi);
+
     // write the output
-    write_output(
-        &args.output,
-        &args.model_coverage,
-        args.bins,
-        args.num_bootstraps,
-        &emi,
-        &header,
-        &counts,
-    )?;
+    write_output(&args.output, json_info, &header, &counts)?;
 
     // if the user requested bootstrap replicates,
     // compute and write those out now.

src/util/oarfish_types.rs

@@ -240,10 +240,44 @@ pub struct InMemoryAlignmentStore<'h> {
 impl<'h> InMemoryAlignmentStore<'h> {
     #[inline]
     pub fn len(&self) -> usize {
-        self.boundaries.len()
+        self.boundaries.len().saturating_sub(1)
     }
 }
 
+pub struct InMemoryAlignmentStoreSamplingWithReplacementIter<'a, 'h, 'b> {
+    pub store: &'a InMemoryAlignmentStore<'h>,
+    pub rand_inds: std::slice::Iter<'b, usize>,
+}
+
+impl<'a, 'b, 'h> Iterator for InMemoryAlignmentStoreSamplingWithReplacementIter<'a, 'b, 'h> {
+    type Item = (&'a [AlnInfo], &'a [f32], &'a [f64]);
+
+    #[inline]
+    fn next(&mut self) -> Option<Self::Item> {
+        if let Some(next_ind) = self.rand_inds.next() {
+            let start = self.store.boundaries[*next_ind];
+            let end = self.store.boundaries[*next_ind + 1];
+            Some((
+                &self.store.alignments[start..end],
+                &self.store.as_probabilities[start..end],
+                &self.store.coverage_probabilities[start..end],
+            ))
+        } else {
+            None
+        }
+    }
+
+    #[inline]
+    fn size_hint(&self) -> (usize, Option<usize>) {
+        (self.rand_inds.len(), Some(self.rand_inds.len()))
+    }
+}
+
+impl<'a, 'b, 'h> ExactSizeIterator
+    for InMemoryAlignmentStoreSamplingWithReplacementIter<'a, 'b, 'h>
+{
+}
+
 pub struct InMemoryAlignmentStoreIter<'a, 'h> {
     pub store: &'a InMemoryAlignmentStore<'h>,
     pub idx: usize,
@@ -267,15 +301,15 @@ impl<'a, 'h> Iterator for InMemoryAlignmentStoreIter<'a, 'h> {
             ))
         }
     }
-}
 
-impl<'a, 'h> ExactSizeIterator for InMemoryAlignmentStoreIter<'a, 'h> {
     #[inline]
-    fn len(&self) -> usize {
-        self.store.boundaries.len()
+    fn size_hint(&self) -> (usize, Option<usize>) {
+        (self.store.len(), Some(self.store.len()))
     }
 }
 
+impl<'a, 'h> ExactSizeIterator for InMemoryAlignmentStoreIter<'a, 'h> {}
+
 impl<'h> InMemoryAlignmentStore<'h> {
     pub fn new(fo: AlignmentFilters, header: &'h Header) -> Self {
         InMemoryAlignmentStore {
@@ -296,6 +330,19 @@ impl<'h> InMemoryAlignmentStore<'h> {
         }
     }
 
+    pub fn random_sampling_iter<'a, 'b>(
+        &'a self,
+        inds: &'b [usize],
+    ) -> InMemoryAlignmentStoreSamplingWithReplacementIter
+    where
+        'b: 'a,
+    {
+        InMemoryAlignmentStoreSamplingWithReplacementIter {
+            store: self,
+            rand_inds: inds.iter(),
+        }
+    }
+
     pub fn add_group<T: sam::alignment::record::Record + std::fmt::Debug>(
         &mut self,
         txps: &mut [TranscriptInfo],
@@ -326,7 +373,7 @@ impl<'h> InMemoryAlignmentStore<'h> {
 
     pub fn num_aligned_reads(&self) -> usize {
         if !self.boundaries.is_empty() {
-            self.boundaries.len() - 1
+            self.len()
         } else {
             0
         }

src/util/write_function.rs

@@ -7,7 +7,7 @@ use arrow2::{
     datatypes::{Field, Schema},
 };
 use path_tools::WithAdditionalExtension;
-use serde_json::json;
+
 use std::path::{Path, PathBuf};
 use std::{
     fs,
@@ -20,10 +20,7 @@ use std::{
 //this part is taken from dev branch
 pub fn write_output(
     output: &PathBuf,
-    prob_flag: &bool,
-    bins: u32,
-    num_bootstraps: u32,
-    em_info: &EMInfo,
+    info: serde_json::Value,
     header: &noodles_sam::header::Header,
     counts: &[f64],
 ) -> io::Result<()> {
@@ -37,21 +34,7 @@ pub fn write_output(
         }
     }
 
-    let prob = if *prob_flag {
-        "binomial"
-    } else {
-        "no_coverage"
-    };
-
     {
-        let info = json!({
-            "prob_model" : prob,
-            "num_bins" : bins,
-            "num_bootstraps" : num_bootstraps,
-            "filter_options" : em_info.eq_map.filter_opts,
-            "discard_table" : em_info.eq_map.discard_table
-        });
-
         let info_path = output.with_additional_extension(".meta_info.json");
         let write = OpenOptions::new()
             .write(true)