[med-svn] [Git][med-team/diamond-aligner][master] 4 commits: New upstream version 2.0.13
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Sun Oct 31 09:57:42 GMT 2021
Nilesh Patra pushed to branch master at Debian Med / diamond-aligner
Commits:
bfb476e4 by Nilesh Patra at 2021-10-31T15:04:29+05:30
New upstream version 2.0.13
- - - - -
58ec570b by Nilesh Patra at 2021-10-31T15:04:33+05:30
Update upstream source from tag 'upstream/2.0.13'
Update to upstream version '2.0.13'
with Debian dir 8d452a2192dc7e4620359fb4a00b4694926a199d
- - - - -
6655e449 by Nilesh Patra at 2021-10-31T09:46:26+00:00
Update manpage
- - - - -
4f9716c6 by Nilesh Patra at 2021-10-31T09:47:02+00:00
Upload to unstable
- - - - -
9 changed files:
- − .travis.yml
- debian/changelog
- + debian/createmanpages
- debian/diamond.1
- 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
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+diamond-aligner (2.0.13-1) unstable; urgency=medium
+
+ * Team Upload.
+ * New upstream version 2.0.13
+ * Update manpage
+
+ -- Nilesh Patra <nilesh at debian.org> Sun, 31 Oct 2021 15:04:59 +0530
+
diamond-aligner (2.0.12-1) unstable; urgency=medium
* Team upload.
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,57 @@
+#!/bin/sh
+
+set -e
+
+if [ ! -x /usr/bin/help2man ]; then
+ echo "E: Missing /usr/bin/help2man, please install it from the cognate package."
+ exit 1
+fi
+
+if [ ! -n "$NAME" ]; then
+ NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+fi
+
+if [ ! -n "$VERSION" ]; then
+ VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+fi
+
+if [ ! -n "$PROGNAME" ]; then
+ PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+fi
+
+MANDIR=debian
+PROGNAME='diamond'
+HELPOPTION='--help'
+
+echo "PROGNAME: '$PROGNAME'"
+echo "NAME: '$NAME'"
+echo "VERSION: '$VERSION'"
+echo "MANDIR: '$MANDIR'"
+echo "HELPOPTION: '$HELPOPTION'"
+
+mkdir -p $MANDIR
+
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr --help-option="$HELPOPTION" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output in '$MANDIR/${progname}.1'.
+To inspect it, try 'nroff -man $MANDIR/${progname}.1'.
+If very unhappy, try passing the HELPOPTION as an environment variable.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
=====================================
debian/diamond.1
=====================================
@@ -1,287 +1,192 @@
-.TH DIAMOND "1" "January 2017" "diamond 0.8.31" "User Commands"
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.48.5.
+.TH DIAMOND "1" "October 2021" "diamond 2.0.13" "User Commands"
.SH NAME
diamond \- accelerated BLAST compatible local sequence aligner
-.SH SYNOPSIS
-.B diamond
-COMMAND [OPTIONS]
.SH DESCRIPTION
- DIAMOND is a sequence aligner for protein and translated DNA searches
- and functions as a drop-in replacement for the NCBI BLAST software
- tools. It is suitable for protein-protein search as well as DNA-protein
- search on short reads and longer sequences including contigs and
- assemblies, providing a speedup of BLAST ranging up to x20,000.
-.SH COMMANDS
-.TP
-makedb
-Build DIAMOND database from a FASTA file
-.TP
-blastp
-Align amino acid query sequences against a protein reference database
-.TP
-blastx
-Align DNA query sequences against a protein reference database
-.TP
-view
-View DIAMOND alignment archive (DAA) formatted file
-.TP
-help
-Produce help message
-.TP
-version
-Display version information
-.TP
-getseq
-Retrieve sequences from a DIAMOND database file
-.SH OPTIONS
-.SS General options:
-.TP
-\fB\-\-threads\fR (\fB\-p\fR)
-number of CPU threads
-.TP
-\fB\-\-db\fR (\fB\-d\fR)
-database file
-.TP
-\fB\-\-out\fR (\fB\-o\fR)
-output file
-.TP
-\fB\-\-outfmt\fR (\fB\-f\fR)
-output format
-.IP
-0 = BLAST pairwise
-.IP
-5 = BLAST XML
-.IP
-6 = BLAST tabular
-.IP
-100 = DIAMOND alignment archive (DAA)
-.IP
-101 = SAM
+diamond v2.0.13.151 (C) Max Planck Society for the Advancement of Science
+Documentation, support and updates available at http://www.diamondsearch.org
+Please cite: http://dx.doi.org/10.1038/s41592\-021\-01101\-x Nature Methods (2021)
+.PP
+Syntax: diamond COMMAND [OPTIONS]
+.PP
+Commands:
+makedb Build DIAMOND database from a FASTA file
+blastp Align amino acid query sequences against a protein reference database
+blastx Align DNA query sequences against a protein reference database
+view View DIAMOND alignment archive (DAA) formatted file
+help Produce help message
+version Display version information
+getseq Retrieve sequences from a DIAMOND database file
+dbinfo Print information about a DIAMOND database file
+test Run regression tests
+makeidx Make database index
+.PP
+General options:
+\fB\-\-threads\fR (\fB\-p\fR) number of CPU threads
+\fB\-\-db\fR (\fB\-d\fR) database file
+\fB\-\-out\fR (\fB\-o\fR) output file
+\fB\-\-outfmt\fR (\fB\-f\fR) output format
+.TP
+0
+= BLAST pairwise
+.TP
+5
+= BLAST XML
+.TP
+6
+= BLAST tabular
+.IP
+100 = DIAMOND alignment archive (DAA)
+101 = SAM
.IP
Value 6 may be followed by a space\-separated list of these keywords:
.IP
-qseqid means Query Seq \- id
-.IP
-qlen means Query sequence length
-.IP
-sseqid means Subject Seq \- id
-.IP
+qseqid means Query Seq \- id
+qlen means Query sequence length
+sseqid means Subject Seq \- id
sallseqid means All subject Seq \- id(s), separated by a ';'
-.IP
slen means Subject sequence length
-.IP
qstart means Start of alignment in query
-.IP
qend means End of alignment in query
-.IP
sstart means Start of alignment in subject
-.IP
send means End of alignment in subject
-.IP
qseq means Aligned part of query sequence
-.IP
+qseq_translated means Aligned part of query sequence (translated)
+full_qseq means Query sequence
+full_qseq_mate means Query sequence of the mate
sseq means Aligned part of subject sequence
-.IP
+full_sseq means Subject sequence
evalue means Expect value
-.IP
bitscore means Bit score
-.IP
score means Raw score
-.IP
length means Alignment length
-.IP
pident means Percentage of identical matches
-.IP
nident means Number of identical matches
-.IP
mismatch means Number of mismatches
-.IP
positive means Number of positive \- scoring matches
-.IP
gapopen means Number of gap openings
-.IP
gaps means Total number of gaps
-.IP
ppos means Percentage of positive \- scoring matches
-.IP
qframe means Query frame
-.IP
btop means Blast traceback operations(BTOP)
-.IP
+cigar means CIGAR string
+staxids means unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)
+sscinames means unique Subject Scientific Name(s), separated by a ';'
+sskingdoms means unique Subject Super Kingdom(s), separated by a ';'
+skingdoms means unique Subject Kingdom(s), separated by a ';'
+sphylums means unique Subject Phylum(s), separated by a ';'
stitle means Subject Title
-.IP
salltitles means All Subject Title(s), separated by a '<>'
-.IP
qcovhsp means Query Coverage Per HSP
-.IP
+scovhsp means Subject Coverage Per HSP
qtitle means Query title
+qqual means Query quality values for the aligned part of the query
+full_qqual means Query quality values
+qstrand means Query strand
.IP
Default: qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore
-.TP
-\fB\-\-verbose\fR (\fB\-v\fR)
-verbose console output
-.TP
-\fB\-\-log\fR
-enable debug log
-.TP
-\fB\-\-quiet\fR
-disable console output
-.SS Makedb options:
-.TP
-\fB\-\-in\fR
-input reference file in FASTA format
-.SS Aligner options:
-.TP
-\fB\-\-query\fR (\fB\-q\fR)
-input query file
-.TP
-\fB\-\-un\fR
-file for unaligned queries
-.TP
-\fB\-\-unal\fR
-report unaligned queries (0=no, 1=yes)
-.TP
-\fB\-\-max\-target\-seqs\fR (\fB\-k\fR)
-maximum number of target sequences to report alignments for
-.TP
-\fB\-\-top\fR
-report alignments within this percentage range of top alignment score (overrides \fB\-\-max\-target\-seqs\fR)
-.TP
-\fB\-\-compress\fR
-compression for output files (0=none, 1=gzip)
-.TP
-\fB\-\-evalue\fR (\fB\-e\fR)
-maximum e\-value to report alignments
-.TP
-\fB\-\-min\-score\fR
-minimum bit score to report alignments (overrides e\-value setting)
-.TP
-\fB\-\-id\fR
-minimum identity% to report an alignment
-.TP
-\fB\-\-query\-cover\fR
-minimum query cover% to report an alignment
-.TP
-\fB\-\-subject\-cover\fR
-minimum subject cover% to report an alignment
-.TP
-\fB\-\-sensitive\fR
-enable sensitive mode (default: fast)
-.TP
-\fB\-\-more\-sensitive\fR
-enable more sensitive mode (default: fast)
-.TP
-\fB\-\-block\-size\fR (\fB\-b\fR)
-sequence block size in billions of letters (default=2.0)
-.TP
-\fB\-\-index\-chunks\fR (\fB\-c\fR)
-number of chunks for index processing
-.TP
-\fB\-\-tmpdir\fR (\fB\-t\fR)
-directory for temporary files
-.TP
-\fB\-\-gapopen\fR
-gap open penalty (default=11 for protein)
-.TP
-\fB\-\-gapextend\fR
-gap extension penalty (default=1 for protein)
-.TP
-\fB\-\-matrix\fR
-score matrix for protein alignment (default=BLOSUM62)
-.TP
-\fB\-\-custom\-matrix\fR
-file containing custom scoring matrix
-.TP
-\fB\-\-lambda\fR
-lambda parameter for custom matrix
-.TP
-\fB\-\-K\fR
-K parameter for custom matrix
-.TP
-\fB\-\-comp\-based\-stats\fR
-enable composition based statistics (0/1=default)
-.TP
-\fB\-\-seg\fR
-enable SEG masking of queries (yes/no)
-.TP
-\fB\-\-query\-gencode\fR
-genetic code to use to translate query (see user manual)
-.TP
-\fB\-\-salltitles\fR
-print full subject titles in output files
-.TP
-\fB\-\-no\-self\-hits\fR
-suppress reporting of identical self hits
-.SS Advanced options:
-.TP
-\fB\-\-min\-orf\fR (\fB\-l\fR)
-ignore translated sequences without an open reading frame of at least this length
-.TP
-\fB\-\-freq\-sd\fR
-number of standard deviations for ignoring frequent seeds
-.TP
-\fB\-\-id2\fR
-minimum number of identities for stage 1 hit
-.TP
-\fB\-\-window\fR (\fB\-w\fR)
-window size for local hit search
-.TP
-\fB\-\-xdrop\fR (\fB\-x\fR)
-xdrop for ungapped alignment
-.TP
-\fB\-\-ungapped\-score\fR
-minimum alignment score to continue local extension
-.TP
-\fB\-\-hit\-band\fR
-band for hit verification
-.TP
-\fB\-\-hit\-score\fR
-minimum score to keep a tentative alignment
-.TP
-\fB\-\-gapped\-xdrop\fR (\fB\-X\fR)
-xdrop for gapped alignment in bits
-.TP
-\fB\-\-band\fR
-band for dynamic programming computation
-.TP
-\fB\-\-shapes\fR (\fB\-s\fR)
-number of seed shapes (0 = all available)
-.TP
-\fB\-\-shape\-mask\fR
-seed shapes
-.TP
-\fB\-\-index\-mode\fR
-index mode (0=4x12, 1=16x9)
-.TP
-\fB\-\-fetch\-size\fR
-trace point fetch size
-.TP
-\fB\-\-rank\-factor\fR
-include subjects within this range of max\-target\-seqs
-.TP
-\fB\-\-rank\-ratio\fR
-include subjects within this ratio of last hit
-.TP
-\fB\-\-max\-hsps\fR
-maximum number of HSPs per subject sequence to save for each query
-.TP
-\fB\-\-dbsize\fR
-effective database size (in letters)
-.TP
-\fB\-\-no\-auto\-append\fR
-disable auto appending of DAA and DMND file extensions
-.TP
-\fB\-\-target\-fetch\-size\fR
-number of target sequences to fetch for seed extension
-.SS View options
-.TP
-\fB\-\-daa\fR (\fB\-a\fR)
-DIAMOND alignment archive (DAA) file
-.TP
-\fB\-\-forwardonly\fR
-only show alignments of forward strand
-.SS Getseq options
-.TP
-\fB\-\-seq\fR
-Sequence numbers to display.
+.PP
+\fB\-\-verbose\fR (\fB\-v\fR) verbose console output
+\fB\-\-log\fR enable debug log
+\fB\-\-quiet\fR disable console output
+\fB\-\-header\fR Write header lines to blast tabular format.
+.PP
+Makedb options:
+\fB\-\-in\fR input reference file in FASTA format
+\fB\-\-taxonmap\fR protein accession to taxid mapping file
+\fB\-\-taxonnodes\fR taxonomy nodes.dmp from NCBI
+\fB\-\-taxonnames\fR taxonomy names.dmp from NCBI
+.PP
+Aligner options:
+\fB\-\-query\fR (\fB\-q\fR) input query file
+\fB\-\-strand\fR query strands to search (both/minus/plus)
+\fB\-\-un\fR file for unaligned queries
+\fB\-\-al\fR file or aligned queries
+\fB\-\-unfmt\fR format of unaligned query file (fasta/fastq)
+\fB\-\-alfmt\fR format of aligned query file (fasta/fastq)
+\fB\-\-unal\fR report unaligned queries (0=no, 1=yes)
+\fB\-\-max\-target\-seqs\fR (\fB\-k\fR) maximum number of target sequences to report alignments for (default=25)
+\fB\-\-top\fR report alignments within this percentage range of top alignment score (overrides \fB\-\-max\-target\-seqs\fR)
+\fB\-\-max\-hsps\fR maximum number of HSPs per target sequence to report for each query (default=1)
+\fB\-\-range\-culling\fR restrict hit culling to overlapping query ranges
+\fB\-\-compress\fR compression for output files (0=none, 1=gzip, zstd)
+\fB\-\-evalue\fR (\fB\-e\fR) maximum e\-value to report alignments (default=0.001)
+\fB\-\-min\-score\fR minimum bit score to report alignments (overrides e\-value setting)
+\fB\-\-id\fR minimum identity% to report an alignment
+\fB\-\-query\-cover\fR minimum query cover% to report an alignment
+\fB\-\-subject\-cover\fR minimum subject cover% to report an alignment
+\fB\-\-fast\fR enable fast mode
+\fB\-\-mid\-sensitive\fR enable mid\-sensitive mode
+\fB\-\-sensitive\fR enable sensitive mode)
+\fB\-\-more\-sensitive\fR enable more sensitive mode
+\fB\-\-very\-sensitive\fR enable very sensitive mode
+\fB\-\-ultra\-sensitive\fR enable ultra sensitive mode
+\fB\-\-iterate\fR iterated search with increasing sensitivity
+\fB\-\-global\-ranking\fR (\fB\-g\fR) number of targets for global ranking
+\fB\-\-block\-size\fR (\fB\-b\fR) sequence block size in billions of letters (default=2.0)
+\fB\-\-index\-chunks\fR (\fB\-c\fR) number of chunks for index processing (default=4)
+\fB\-\-tmpdir\fR (\fB\-t\fR) directory for temporary files
+\fB\-\-parallel\-tmpdir\fR directory for temporary files used by multiprocessing
+\fB\-\-gapopen\fR gap open penalty
+\fB\-\-gapextend\fR gap extension penalty
+\fB\-\-frameshift\fR (\fB\-F\fR) frame shift penalty (default=disabled)
+\fB\-\-long\-reads\fR short for \fB\-\-range\-culling\fR \fB\-\-top\fR 10 \fB\-F\fR 15
+\fB\-\-matrix\fR score matrix for protein alignment (default=BLOSUM62)
+\fB\-\-custom\-matrix\fR file containing custom scoring matrix
+\fB\-\-comp\-based\-stats\fR composition based statistics mode (0\-4)
+\fB\-\-masking\fR masking algorithm (none, seg, tantan=default)
+\fB\-\-query\-gencode\fR genetic code to use to translate query (see user manual)
+\fB\-\-salltitles\fR include full subject titles in DAA file
+\fB\-\-sallseqid\fR include all subject ids in DAA file
+\fB\-\-no\-self\-hits\fR suppress reporting of identical self hits
+\fB\-\-taxonlist\fR restrict search to list of taxon ids (comma\-separated)
+\fB\-\-taxon\-exclude\fR exclude list of taxon ids (comma\-separated)
+\fB\-\-seqidlist\fR filter the database by list of accessions
+\fB\-\-skip\-missing\-seqids\fR ignore accessions missing in the database
+.PP
+Advanced options:
+\fB\-\-algo\fR Seed search algorithm (0=double\-indexed/1=query\-indexed/ctg=contiguous\-seed)
+\fB\-\-bin\fR number of query bins for seed search
+\fB\-\-min\-orf\fR (\fB\-l\fR) ignore translated sequences without an open reading frame of at least this length
+\fB\-\-seed\-cut\fR cutoff for seed complexity
+\fB\-\-freq\-masking\fR mask seeds based on frequency
+\fB\-\-freq\-sd\fR number of standard deviations for ignoring frequent seeds
+\fB\-\-motif\-masking\fR softmask abundant motifs (0/1)
+\fB\-\-id2\fR minimum number of identities for stage 1 hit
+\fB\-\-xdrop\fR (\fB\-x\fR) xdrop for ungapped alignment
+\fB\-\-gapped\-filter\-evalue\fR E\-value threshold for gapped filter (auto)
+\fB\-\-band\fR band for dynamic programming computation
+\fB\-\-shapes\fR (\fB\-s\fR) number of seed shapes (default=all available)
+\fB\-\-shape\-mask\fR seed shapes
+\fB\-\-multiprocessing\fR enable distributed\-memory parallel processing
+\fB\-\-mp\-init\fR initialize multiprocessing run
+\fB\-\-mp\-recover\fR enable continuation of interrupted multiprocessing run
+\fB\-\-mp\-query\-chunk\fR process only a single query chunk as specified
+\fB\-\-ext\-chunk\-size\fR chunk size for adaptive ranking (default=auto)
+\fB\-\-no\-ranking\fR disable ranking heuristic
+\fB\-\-ext\fR Extension mode (banded\-fast/banded\-slow/full)
+\fB\-\-culling\-overlap\fR minimum range overlap with higher scoring hit to delete a hit (default=50%)
+\fB\-\-taxon\-k\fR maximum number of targets to report per species
+\fB\-\-range\-cover\fR percentage of query range to be covered for range culling (default=50%)
+\fB\-\-dbsize\fR effective database size (in letters)
+\fB\-\-no\-auto\-append\fR disable auto appending of DAA and DMND file extensions
+\fB\-\-xml\-blord\-format\fR Use gnl|BL_ORD_ID| style format in XML output
+\fB\-\-stop\-match\-score\fR Set the match score of stop codons against each other.
+\fB\-\-tantan\-minMaskProb\fR minimum repeat probability for masking (default=0.9)
+\fB\-\-file\-buffer\-size\fR file buffer size in bytes (default=67108864)
+\fB\-\-memory\-limit\fR (\fB\-M\fR) Memory limit for extension stage in GB
+\fB\-\-no\-unlink\fR Do not unlink temporary files.
+\fB\-\-target\-indexed\fR Enable target\-indexed mode
+\fB\-\-ignore\-warnings\fR Ignore warnings
+.PP
+View options:
+\fB\-\-daa\fR (\fB\-a\fR) DIAMOND alignment archive (DAA) file
+\fB\-\-forwardonly\fR only show alignments of forward strand
+.PP
+Getseq options:
+\fB\-\-seq\fR Space\-separated list of sequence numbers to display.
+.PP
+Online documentation at http://www.diamondsearch.org
.SH AUTHOR
-This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
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/-/compare/f68bee9e79c1abb3c34db94ee7fc11ba3b13eb74...4f9716c6d5a0e2676905d5a5f244e390c6773187
--
View it on GitLab: https://salsa.debian.org/med-team/diamond-aligner/-/compare/f68bee9e79c1abb3c34db94ee7fc11ba3b13eb74...4f9716c6d5a0e2676905d5a5f244e390c6773187
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