Nilesh Patra pushed to branch upstream at Debian Med / diamond-aligner
Commits:
bfb476e4 by Nilesh Patra at 2021-10-31T15:04:29+05:30
New upstream version 2.0.13
- - - - -
6 changed files:
- − .travis.yml
- src/ChangeLog
- src/align/gapped_score.cpp
- src/basic/basic.cpp
- src/basic/const.h
- src/dp/swipe/banded_3frame_swipe.cpp
Changes:
=====================================
.travis.yml deleted
=====================================
@@ -1,36 +0,0 @@
-os:
- - linux
- - osx
-
-dist:
-# - xenial
- - trusty
-
-language: c++
-
-#addons:
-# apt:
-# packages:
-# - gdb
-# - libclang-common-6.0-dev
-
-arch:
- - amd64
- - arm64
- - ppc64le
- - s390x
-
-compiler:
- - g++
-# - clang
-
-install: skip
-
-script:
- - mkdir build
- - cd build
- - cmake -DCMAKE_BUILD_TYPE=Release ..
- - make
-# - gdb --ex=r -return-child-result -batch -ex bt --args ./diamond test
-# - lldb --batch --one-line r --one-line-on-crash bt -- ./diamond test
- - ./diamond test
\ No newline at end of file
=====================================
src/ChangeLog
=====================================
@@ -1,3 +1,6 @@
+[2.0.13]
+- Fixed a bug that caused invalid bit scores in frameshift alignment mode.
+
[2.0.12]
- Fixed an error when using HSP filter settings together with a BLAST database.
- Optimized the performance of alignment traceback.
=====================================
src/align/gapped_score.cpp
=====================================
@@ -106,7 +106,7 @@ static void add_dp_targets(const WorkTarget& target, int
target_idx, const Seque
if (target.hsp[frame].empty())
continue;
- int d0 = INT_MAX, d1 = INT_MIN, j0 = INT_MAX, j1 = INT_MIN,
bits = 0;
+ int d0 = INT_MAX, d1 = INT_MIN, score = 0;
for (const Hsp_traits &hsp : target.hsp[frame]) {
const int b0 = std::max(hsp.d_min - band, -(slen - 1)),
@@ -115,24 +115,23 @@ static void add_dp_targets(const WorkTarget& target, int
target_idx, const Seque
if (overlap / (d1 - d0) > config.min_band_overlap ||
overlap / (b1 - b0) > config.min_band_overlap) {
d0 = std::min(d0, b0);
d1 = std::max(d1, b1);
- j0 = std::min(j0, hsp.subject_range.begin_);
- j1 = std::max(j1, hsp.subject_range.end_);
- const int64_t dp_size =
(int64_t)DpTarget::banded_cols(qlen, slen, d0, d1) * int64_t(d1 - d0);
- bits = std::max(bits,
(int)DP::BandedSwipe::bin(hsp_values, d1 - d0, 0, hsp.score, dp_size,
score_width, 0));
+ score = std::max(score, hsp.score);
}
else {
- if (d0 != INT_MAX)
-
dp_targets[frame][bits].emplace_back(target.seq, slen, d0, d1, target_idx,
qlen, matrix);
+ if (d0 != INT_MAX) {
+ const int64_t dp_size =
(int64_t)DpTarget::banded_cols(qlen, slen, d0, d1) * int64_t(d1 - d0);
+ const auto bin =
DP::BandedSwipe::bin(hsp_values, d1 - d0, 0, score, dp_size, score_width, 0);
+
dp_targets[frame][bin].emplace_back(target.seq, slen, d0, d1, target_idx, qlen,
matrix);
+ }
d0 = b0;
d1 = b1;
- j0 = hsp.subject_range.begin_;
- j1 = hsp.subject_range.end_;
- const int64_t dp_size =
(int64_t)DpTarget::banded_cols(qlen, slen, d0, d1) * int64_t(d1 - d0);
- bits = (int)DP::BandedSwipe::bin(hsp_values, d1
- d0, 0, hsp.score, dp_size, score_width, 0);
+ score = hsp.score;
}
}
- dp_targets[frame][bits].emplace_back(target.seq, slen, d0, d1,
target_idx, qlen, matrix);
+ const int64_t dp_size = (int64_t)DpTarget::banded_cols(qlen,
slen, d0, d1) * int64_t(d1 - d0);
+ const auto bin = DP::BandedSwipe::bin(hsp_values, d1 - d0, 0,
score, dp_size, score_width, 0);
+ dp_targets[frame][bin].emplace_back(target.seq, slen, d0, d1,
target_idx, qlen, matrix);
}
}
=====================================
src/basic/basic.cpp
=====================================
@@ -29,7 +29,7 @@ along with this program. If not, see
<http://www.gnu.org/licenses/>.
#include "../util/util.h"
#include "../stats/standard_matrix.h"
-const char* Const::version_string = "2.0.12";
+const char* Const::version_string = "2.0.13";
const char* Const::program_name = "diamond";
Align_mode::Align_mode(unsigned mode) :
=====================================
src/basic/const.h
=====================================
@@ -25,7 +25,7 @@ struct Const
{
enum {
- build_version = 150,
+ build_version = 151,
#ifdef SINGLE_THREADED
seedp_bits = 0,
#else
=====================================
src/dp/swipe/banded_3frame_swipe.cpp
=====================================
@@ -337,6 +337,7 @@ Hsp traceback(Sequence *query, Strand strand, int dna_len,
const Banded3FrameSwi
Hsp out(true);
out.swipe_target = target.target_idx;
out.score = ScoreTraits<_sv>::int_score(max_score) *
config.cbs_matrix_scale;
+ out.bit_score = score_matrix.bitscore(out.score);
out.evalue = evalue;
out.transcript.reserve(size_t(out.score *
config.transcript_len_estimate));
@@ -378,6 +379,7 @@ Hsp traceback(Sequence *query, Strand strand, int dna_len,
const Banded3FrameSwi
const int j0 = i1 - (target.d_end - 1);
out.swipe_target = target.target_idx;
out.score = ScoreTraits<_sv>::int_score(max_score) *
config.cbs_matrix_scale;
+ out.bit_score = score_matrix.bitscore(out.score);
out.evalue = evalue;
out.query_range.end_ = std::min(i0 + max_col + (int)dp.band() / 3 / 2,
(int)query[0].length());
out.query_range.begin_ = std::max(out.query_range.end_ - (j0 +
max_col), 0);
View it on GitLab:
https://salsa.debian.org/med-team/diamond-aligner/-/commit/bfb476e4a522c45a09fba4c73f6e0962135133ce
--
View it on GitLab:
https://salsa.debian.org/med-team/diamond-aligner/-/commit/bfb476e4a522c45a09fba4c73f6e0962135133ce
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