From e2b16e35d4094a2133f6d2c0fb6ef65c63f8719b Mon Sep 17 00:00:00 2001 From: Anton Korobeynikov Date: Wed, 30 Oct 2024 22:38:36 +0300 Subject: [PATCH 1/2] Disable seq length limit --- ext/src/hmmer/src/p7_pipeline.c | 2 ++ 1 file changed, 2 insertions(+) diff --git a/ext/src/hmmer/src/p7_pipeline.c b/ext/src/hmmer/src/p7_pipeline.c index a276d4cb5e..6edf15acac 100644 --- a/ext/src/hmmer/src/p7_pipeline.c +++ b/ext/src/hmmer/src/p7_pipeline.c @@ -711,7 +711,9 @@ p7_Pipeline(P7_PIPELINE *pli, P7_OPROFILE *om, P7_BG *bg, const ESL_SQ *sq, cons int status; if (sq->n == 0) return eslOK; /* silently skip length 0 seqs; they'd cause us all sorts of weird problems */ +#if 0 // SPADES_LOCAL: disable if (sq->n > 100000) ESL_EXCEPTION(eslETYPE, "Target sequence length > 100K, over comparison pipeline limit.\n(Did you mean to use nhmmer/nhmmscan?)"); +#endif p7_omx_GrowTo(pli->oxf, om->M, 0, sq->n); /* expand the one-row omx if needed */ From 356ace3dfc2d57030ea32d86e87de2a0c666e013 Mon Sep 17 00:00:00 2001 From: Anton Korobeynikov Date: Wed, 30 Oct 2024 22:38:53 +0300 Subject: [PATCH 2/2] Unbreak build --- ext/src/lexy/include/lexy/input_location.hpp | 2 +- src/common/adt/flat_map.hpp | 2 +- src/common/adt/flat_set.hpp | 2 +- src/common/kmer_index/ph_map/key_with_hash.hpp | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/ext/src/lexy/include/lexy/input_location.hpp b/ext/src/lexy/include/lexy/input_location.hpp index 55f6edb78f..983d2aa022 100644 --- a/ext/src/lexy/include/lexy/input_location.hpp +++ b/ext/src/lexy/include/lexy/input_location.hpp @@ -180,7 +180,7 @@ class input_location { if (lhs._line_nr != rhs._line_nr) return lhs._line_nr < rhs._line_nr; - return lhs._column_nr < rhs._colum_nr; + return lhs._column_nr < rhs._column_nr; } friend constexpr bool operator<=(const input_location& lhs, const input_location& rhs) { diff --git a/src/common/adt/flat_map.hpp b/src/common/adt/flat_map.hpp index f272d36535..f868e9afb3 100644 --- a/src/common/adt/flat_map.hpp +++ b/src/common/adt/flat_map.hpp @@ -180,7 +180,7 @@ struct flat_map { } void swap(flat_map &other) { - data_.swap(other.data); + data_.swap(other.data_); } void clear() { diff --git a/src/common/adt/flat_set.hpp b/src/common/adt/flat_set.hpp index 23c41f7c9c..249135fddf 100644 --- a/src/common/adt/flat_set.hpp +++ b/src/common/adt/flat_set.hpp @@ -131,7 +131,7 @@ struct flat_set { return data_.erase(iterator_const_cast(first), iterator_const_cast(last)); } - void swap(flat_set &other) { data_.swap(other.data); } + void swap(flat_set &other) { data_.swap(other.data_); } void clear() { data_.clear(); } diff --git a/src/common/kmer_index/ph_map/key_with_hash.hpp b/src/common/kmer_index/ph_map/key_with_hash.hpp index 3727d4ad54..9a92e70206 100644 --- a/src/common/kmer_index/ph_map/key_with_hash.hpp +++ b/src/common/kmer_index/ph_map/key_with_hash.hpp @@ -62,7 +62,7 @@ class SimpleKeyWithHash { bool operator==(const SimpleKeyWithHash &that) const { VERIFY_DEV(&this->hash_ == &that.hash_); if (this->ready_ && that.ready_) - return this->idx_ == that.idx_ && this->is_minimal_ == that.is_minimal_; + return this->idx_ == that.idx_; return this->key_ == that.key_; }