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Fix warnings #85

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merged 1 commit into from
Nov 5, 2024
Merged

Fix warnings #85

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2 changes: 1 addition & 1 deletion src/exports/gfa.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ pub fn export_gfa(
let boundary_edges = Edge::boundary_edges_from_sequences(&blocks);
edges.extend(boundary_edges.clone());

let (mut graph, edges_by_node_pair) = Edge::build_graph(&edges, &blocks);
let (mut graph, _edges_by_node_pair) = Edge::build_graph(&edges, &blocks);

BlockGroup::prune_graph(&mut graph);

Expand Down
8 changes: 2 additions & 6 deletions src/graph.rs
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@@ -1,15 +1,11 @@
use std::collections::{HashMap, HashSet, VecDeque};
use std::collections::{HashSet, VecDeque};
use std::fmt::Debug;
use std::hash::Hash;
use std::iter::from_fn;

use crate::models::strand::Strand;
use petgraph::graphmap::DiGraphMap;
use petgraph::prelude::EdgeRef;
use petgraph::visit::{
GraphBase, GraphRef, IntoEdgeReferences, IntoEdges, IntoNeighbors, IntoNeighborsDirected,
NodeCount,
};
use petgraph::visit::{GraphRef, IntoEdges, IntoNeighbors, IntoNeighborsDirected, NodeCount};
use petgraph::Direction;

#[derive(Clone, Copy, Debug, Eq, PartialEq, Hash, Ord, PartialOrd)]
Expand Down
10 changes: 5 additions & 5 deletions src/models/accession.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -102,9 +102,9 @@ impl Accession {
) -> Accession {
match Accession::create(conn, name, path_id, parent_accession_id) {
Ok(accession) => accession,
Err(rusqlite::Error::SqliteFailure(err, details)) => {
Err(rusqlite::Error::SqliteFailure(err, _details)) => {
if err.code == rusqlite::ErrorCode::ConstraintViolation {
let mut existing_id: i64;
let existing_id: i64;
if let Some(id) = parent_accession_id {
existing_id = conn.query_row("select id from accessions where name = ?1 and path_id = ?2 and parent_accession_id = ?3;", params_from_iter(vec![Value::from(name.to_string()), Value::from(path_id), Value::from(id)]), |row| row.get(0)).unwrap();
} else {
Expand Down Expand Up @@ -157,7 +157,7 @@ impl AccessionEdge {
row.get(0)
}) {
Ok(res) => res,
Err(rusqlite::Error::SqliteFailure(err, details)) => {
Err(rusqlite::Error::SqliteFailure(_err, _details)) => {
conn.query_row("select id from accession_edges where source_node_id = ?1 source_coordinate = ?2 source_strand = ?3 target_node_id = ?4 target_coordinate = ?5 target_strand = ?6 chromosome_index = ?7", params_from_iter(&placeholders), |row| {
row.get(0)
}).unwrap()
Expand Down Expand Up @@ -326,9 +326,9 @@ mod tests {
#[test]
fn test_accession_create_query() {
let conn = &get_connection(None);
let (bg, path) = setup_block_group(conn);
let (_bg, path) = setup_block_group(conn);
let accession = Accession::create(conn, "test", path.id, None).unwrap();
let accession_2 = Accession::create(conn, "test2", path.id, None).unwrap();
let _accession_2 = Accession::create(conn, "test2", path.id, None).unwrap();
assert_eq!(
Accession::query(
conn,
Expand Down
23 changes: 11 additions & 12 deletions src/models/block_group.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@ use interavl::IntervalTree as IT2;
use intervaltree::IntervalTree;
use itertools::Itertools;
use petgraph::graphmap::DiGraphMap;
use petgraph::visit::Bfs;
use petgraph::Direction;
use rusqlite::{params_from_iter, types::Value as SQLValue, Connection};
use serde::{Deserialize, Serialize};
Expand Down Expand Up @@ -882,7 +881,7 @@ mod tests {
);

Sample::create(conn, "sample2");
let bg2 =
let _bg2 =
BlockGroup::get_or_create_sample_block_group(conn, "test", "sample2", "chr1", None)
.unwrap();
assert_eq!(
Expand Down Expand Up @@ -1765,7 +1764,7 @@ mod tests {
fn test_blockgroup_interval_tree() {
let conn = &get_connection(None);
let (block_group_id, path) = setup_block_group(conn);
let new_sample = Sample::create(conn, "child");
let _new_sample = Sample::create(conn, "child");
let new_bg_id =
BlockGroup::get_or_create_sample_block_group(conn, "test", "child", "chr1", None)
.unwrap();
Expand Down Expand Up @@ -1942,8 +1941,8 @@ mod tests {
#[test]
fn test_changes_against_derivative_blockgroups() {
let conn = &get_connection(None);
let (block_group_id, path) = setup_block_group(conn);
let new_sample = Sample::create(conn, "child");
let (_block_group_id, _path) = setup_block_group(conn);
let _new_sample = Sample::create(conn, "child");
let new_bg_id =
BlockGroup::get_or_create_sample_block_group(conn, "test", "child", "chr1", None)
.unwrap();
Expand Down Expand Up @@ -1987,7 +1986,7 @@ mod tests {
);

// Now, we make a change against another descendant
let new_sample = Sample::create(conn, "grandchild");
let _new_sample = Sample::create(conn, "grandchild");
let gc_bg_id = BlockGroup::get_or_create_sample_block_group(
conn,
"test",
Expand Down Expand Up @@ -2037,8 +2036,8 @@ mod tests {
// This test ensures that if we have heterozygous changes that do not introduce frameshifts,
// we can modify regions downstream of them.
let conn = &get_connection(None);
let (block_group_id, path) = setup_block_group(conn);
let new_sample = Sample::create(conn, "child");
let (_block_group_id, _path) = setup_block_group(conn);
let _new_sample = Sample::create(conn, "child");
let new_bg_id =
BlockGroup::get_or_create_sample_block_group(conn, "test", "child", "chr1", None)
.unwrap();
Expand Down Expand Up @@ -2085,7 +2084,7 @@ mod tests {
);

// Now, we make a change against another descendant
let new_sample = Sample::create(conn, "grandchild");
let _new_sample = Sample::create(conn, "grandchild");
let gc_bg_id = BlockGroup::get_or_create_sample_block_group(
conn,
"test",
Expand Down Expand Up @@ -2147,8 +2146,8 @@ mod tests {
fn test_prohibits_out_of_frame_changes_against_derivative_diploid_blockgroups() {
// This test ensures that we do not allow ambiguous changes by coordinates
let conn = &get_connection(None);
let (block_group_id, path) = setup_block_group(conn);
let new_sample = Sample::create(conn, "child");
let (_block_group_id, _path) = setup_block_group(conn);
let _new_sample = Sample::create(conn, "child");
let new_bg_id =
BlockGroup::get_or_create_sample_block_group(conn, "test", "child", "chr1", None)
.unwrap();
Expand Down Expand Up @@ -2197,7 +2196,7 @@ mod tests {
);

// Now, we make a change against another descendant and get an error
let new_sample = Sample::create(conn, "grandchild");
let _new_sample = Sample::create(conn, "grandchild");
let gc_bg_id = BlockGroup::get_or_create_sample_block_group(
conn,
"test",
Expand Down
6 changes: 3 additions & 3 deletions src/test_helpers.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -159,14 +159,14 @@ pub fn save_graph(graph: &DiGraphMap<GraphNode, GraphEdge>, path: &str) {
use petgraph::dot::{Config, Dot};
use std::fs::File;
let mut file = File::create(path).unwrap();
file.write_all(
let _ = file.write_all(
format!(
"{dot:?}",
dot = Dot::with_attr_getters(
&graph,
&[Config::NodeNoLabel, Config::EdgeNoLabel],
&|_, (_, _, edge_weight)| format!("label = \"{}\"", edge_weight.chromosome_index),
&|_, (node, weight)| format!(
&|_, (node, _weight)| format!(
"label = \"{}[{}-{}]\"",
node.node_id, node.sequence_start, node.sequence_end
),
Expand All @@ -191,8 +191,8 @@ where

pub fn get_sample_bg<'a>(conn: &Connection, sample_name: impl Into<Option<&'a str>>) -> BlockGroup {
let sample_name = sample_name.into();
let mut query = "";
let mut placeholders = vec![];
let query;
if let Some(name) = sample_name {
query = "select * from block_groups where sample_name = ?1";
placeholders.push(Value::from(name.to_string()));
Expand Down
13 changes: 6 additions & 7 deletions src/updates/vcf.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ use noodles::vcf::variant::record::info::field::Value as InfoValue;
use noodles::vcf::variant::record::samples::series::value::genotype::Phasing;
use noodles::vcf::variant::record::samples::series::Value;
use noodles::vcf::variant::record::samples::Sample as NoodlesSample;
use noodles::vcf::variant::record::{AlternateBases, ReferenceBases};
use noodles::vcf::variant::record::AlternateBases;
use noodles::vcf::variant::Record;
use rusqlite::{session, types::Value as SQLValue, Connection};

Expand Down Expand Up @@ -218,7 +218,7 @@ pub fn update_with_vcf<'a>(
let seq_name: String = record.reference_sequence_name().to_string();
let ref_seq = record.reference_bases();
// this converts the coordinates to be zero based, start inclusive, end exclusive
let mut ref_end = record.variant_end(&header).unwrap().get() as i64;
let ref_end = record.variant_end(&header).unwrap().get() as i64;
let alt_bases = record.alternate_bases();
let alt_alleles: Vec<_> = alt_bases.iter().collect::<io::Result<_>>().unwrap();
let mut vcf_entries = vec![];
Expand All @@ -238,7 +238,7 @@ pub fn update_with_vcf<'a>(
};

if !fixed_sample.is_empty() && !genotype.is_empty() {
let mut sample_bg_id = BlockGroupCache::lookup(
let sample_bg_id = BlockGroupCache::lookup(
&mut block_group_cache,
collection_name,
&fixed_sample,
Expand All @@ -251,7 +251,7 @@ pub fn update_with_vcf<'a>(
if let Some(gt) = genotype {
let allele_accession = accession_name
.clone()
.filter(|name| gt.allele as i32 == accession_allele);
.filter(|_| gt.allele as i32 == accession_allele);
let mut ref_start = (record.variant_start().unwrap().unwrap().get() - 1) as i64;
if gt.allele != 0 {
let mut alt_seq = alt_alleles[chromosome_index - 1];
Expand Down Expand Up @@ -295,7 +295,7 @@ pub fn update_with_vcf<'a>(
}
} else {
for (sample_index, sample) in record.samples().iter().enumerate() {
let mut sample_bg_id = BlockGroupCache::lookup(
let sample_bg_id = BlockGroupCache::lookup(
&mut block_group_cache,
collection_name,
&sample_names[sample_index],
Expand All @@ -320,7 +320,7 @@ pub fn update_with_vcf<'a>(
if let Some(allele) = allele {
let allele_accession = accession_name
.clone()
.filter(|name| allele as i32 == accession_allele);
.filter(|_| allele as i32 == accession_allele);
if allele != 0 {
let mut alt_seq = alt_alleles[allele - 1];
if alt_seq != "*" && alt_seq.len() < ref_seq.len() {
Expand Down Expand Up @@ -459,7 +459,6 @@ mod tests {
// Note this useful idiom: importing names from outer (for mod tests) scope.
use super::*;
use crate::imports::fasta::import_fasta;
use crate::imports::gfa::import_gfa;
use crate::models::accession::Accession;
use crate::models::node::Node;
use crate::models::operations::setup_db;
Expand Down