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seqtohashes errors instead of panic for frame errors #3445

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merged 4 commits into from
Dec 20, 2024
Merged

seqtohashes errors instead of panic for frame errors #3445

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7905ac2
seqtohashes errors instead of panic for frame errors
bluegenes Dec 20, 2024
e2f7b1c
clippy fix
bluegenes Dec 20, 2024
a7697ba
rustfmt
bluegenes Dec 20, 2024
30b524e
update include/sourmash.h
ctb Dec 20, 2024
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3 changes: 3 additions & 0 deletions include/sourmash.h
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,9 @@ enum SourmashErrorCode {
SOURMASH_ERROR_CODE_INVALID_PROT = 1102,
SOURMASH_ERROR_CODE_INVALID_CODON_LENGTH = 1103,
SOURMASH_ERROR_CODE_INVALID_HASH_FUNCTION = 1104,
SOURMASH_ERROR_CODE_INVALID_SKIPMER_FRAME = 1105,
SOURMASH_ERROR_CODE_INVALID_SKIPMER_SIZE = 1106,
SOURMASH_ERROR_CODE_INVALID_TRANSLATE_FRAME = 1107,
SOURMASH_ERROR_CODE_READ_DATA = 1201,
SOURMASH_ERROR_CODE_STORAGE = 1202,
SOURMASH_ERROR_CODE_HLL_PRECISION_BOUNDS = 1301,
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15 changes: 15 additions & 0 deletions src/core/src/errors.rs
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Expand Up @@ -55,6 +55,15 @@ pub enum SourmashError {
#[error("Codon is invalid length: {message}")]
InvalidCodonLength { message: String },

#[error("Skipmer ksize must be >= n ({n}), but got ksize: {ksize}")]
InvalidSkipmerSize { ksize: usize, n: usize },

#[error("Skipmer frame number must be < n ({n}), but got start: {start}")]
InvalidSkipmerFrame { start: usize, n: usize },

#[error("Frame number must be 0, 1, or 2, but got {frame_number}")]
InvalidTranslateFrame { frame_number: usize },

#[error("Set error rate to a value smaller than 0.367696 and larger than 0.00203125")]
HLLPrecisionBounds,

Expand Down Expand Up @@ -125,6 +134,9 @@ pub enum SourmashErrorCode {
InvalidProt = 11_02,
InvalidCodonLength = 11_03,
InvalidHashFunction = 11_04,
InvalidSkipmerFrame = 11_05,
InvalidSkipmerSize = 11_06,
InvalidTranslateFrame = 11_07,
// index-related errors
ReadData = 12_01,
Storage = 12_02,
Expand Down Expand Up @@ -166,6 +178,9 @@ impl SourmashErrorCode {
SourmashError::InvalidProt { .. } => SourmashErrorCode::InvalidProt,
SourmashError::InvalidCodonLength { .. } => SourmashErrorCode::InvalidCodonLength,
SourmashError::InvalidHashFunction { .. } => SourmashErrorCode::InvalidHashFunction,
SourmashError::InvalidSkipmerFrame { .. } => SourmashErrorCode::InvalidSkipmerFrame,
SourmashError::InvalidSkipmerSize { .. } => SourmashErrorCode::InvalidSkipmerSize,
SourmashError::InvalidTranslateFrame { .. } => SourmashErrorCode::InvalidTranslateFrame,
SourmashError::ReadDataError { .. } => SourmashErrorCode::ReadData,
SourmashError::StorageError { .. } => SourmashErrorCode::Storage,
SourmashError::HLLPrecisionBounds { .. } => SourmashErrorCode::HLLPrecisionBounds,
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15 changes: 13 additions & 2 deletions src/core/src/ffi/minhash.rs
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Expand Up @@ -73,15 +73,26 @@

let mut output: Vec<u64> = Vec::with_capacity(insize);

// Call SeqToHashes::new and handle errors
let ready_hashes = SeqToHashes::new(

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buf,
mh.ksize(),
force,
is_protein,

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mh.hash_function(),
mh.seed(),
)?;


if force && bad_kmers_as_zeroes{
for hash_value in SeqToHashes::new(buf, mh.ksize(), force, is_protein, mh.hash_function(), mh.seed()){
for hash_value in ready_hashes{

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match hash_value{
Ok(x) => output.push(x),
Err(err) => return Err(err),
}
}
}else{
for hash_value in SeqToHashes::new(buf, mh.ksize(), force, is_protein, mh.hash_function(), mh.seed()){
for hash_value in ready_hashes {

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match hash_value{
Ok(0) => continue,
Ok(x) => output.push(x),
Expand Down
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