[med-svn] [Git][med-team/last-align][master] 7 commits: New upstream version 1645
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Sun Sep 28 11:11:07 BST 2025
Nilesh Patra pushed to branch master at Debian Med / last-align
Commits:
9c6df2d3 by Nilesh Patra at 2025-09-28T15:04:44+05:30
New upstream version 1645
- - - - -
33ca566c by Nilesh Patra at 2025-09-28T15:04:47+05:30
Update upstream source from tag 'upstream/1645'
Update to upstream version '1645'
with Debian dir 68be21ef74800b42a2fea917e153c1f59279ab42
- - - - -
7ff82b21 by Nilesh Patra at 2025-09-28T15:05:19+05:30
Diable build for i386 in salsa CI
- - - - -
f7b1a07f by Nilesh Patra at 2025-09-28T15:05:54+05:30
Drop myself from uploaders
- - - - -
7ff2be43 by Nilesh Patra at 2025-09-28T15:06:09+05:30
Drop Rules-Requires-Root field
- - - - -
b81a964e by Nilesh Patra at 2025-09-28T15:18:31+05:30
Drop Redundant B-D on debhelper
- - - - -
32707769 by Nilesh Patra at 2025-09-28T15:32:43+05:30
Upload to unstable
- - - - -
11 changed files:
- bin/maf-convert
- debian/changelog
- debian/control
- debian/salsa-ci.yml
- src/GappedXdropAligner.cc
- src/GappedXdropAlignerDna.cc
- src/GappedXdropAlignerPssm.cc
- src/makefile
- src/mcf_big_seq.hh
- src/split/cbrc_split_aligner.cc
- test/maf-convert-test.out
Changes:
=====================================
bin/maf-convert
=====================================
@@ -383,6 +383,7 @@ def writeChain(maf):
else:
size = i
print(size)
+ print()
def mafConvertToChain(opts, lines):
for maf in mafInput(opts, lines):
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+last-align (1645-1) unstable; urgency=medium
+
+ * Team Upload.
+ * New upstream version 1645
+ * Drop myself from uploaders
+ * Drop Rules-Requires-Root field
+ * Drop Redundant B-D on debhelper
+
+ -- Nilesh Patra <nilesh at debian.org> Sun, 28 Sep 2025 15:32:21 +0530
+
last-align (1642-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
@@ -1,8 +1,7 @@
Source: last-align
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy at debian.org>,
- Andreas Tille <tille at debian.org>,
- Nilesh Patra <nilesh at debian.org>
+ Andreas Tille <tille at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
@@ -10,13 +9,11 @@ Build-Depends: debhelper-compat (= 13),
python3-pil,
zlib1g-dev,
libsimde-dev,
- debhelper,
architecture-is-64-bit
Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/last-align
Vcs-Git: https://salsa.debian.org/med-team/last-align.git
Homepage: https://gitlab.com/mcfrith/last
-Rules-Requires-Root: no
Package: last-align
Architecture: any
=====================================
debian/salsa-ci.yml
=====================================
@@ -5,4 +5,5 @@ include:
variables:
SALSA_CI_DISABLE_BLHC: 1
+ SALSA_CI_DISABLE_BUILD_PACKAGE_I386: 1
# SALSA_CI_DISABLE_REPROTEST: 1
=====================================
src/GappedXdropAligner.cc
=====================================
@@ -94,8 +94,8 @@ int GappedXdropAligner::align(BigPtr seq1,
for (int i = 0; i < simdLen; ++i) {
const int *x = scorer[*seq1];
- pssmQueue.push(x, i);
seq1 += seqIncrement * !isDelimiter(0, x);
+ pssmQueue.push(x, i);
seq2queue.push(*seq2, i);
}
@@ -201,8 +201,8 @@ int GappedXdropAligner::align(BigPtr seq1,
++numCells;
++seq1end;
const int *x = scorer[*seq1];
- pssmQueue.push(x, n + simdLen);
seq1 += seqIncrement * !isDelimiter(0, x);
+ pssmQueue.push(x, n + simdLen);
isDelimiter1 = isDelimiter(0, pssmQueue.fromEnd(simdLen));
}
=====================================
src/GappedXdropAlignerDna.cc
=====================================
@@ -74,8 +74,8 @@ int GappedXdropAligner::alignDna(BigPtr seq1,
for (int i = 0; i < seqLoadLen; ++i) {
uchar x = toUnmasked[*seq1];
- seq1queue.push(x, i);
seq1 += seqIncrement * (x != delimiter);
+ seq1queue.push(x, i);
seq2queue.push(toUnmasked[*seq2], i);
}
@@ -198,8 +198,8 @@ int GappedXdropAligner::alignDna(BigPtr seq1,
++numCells;
++seq1end;
uchar x = toUnmasked[*seq1];
- seq1queue.push(x, n + seqLoadLen);
seq1 += seqIncrement * (x != delimiter);
+ seq1queue.push(x, n + seqLoadLen);
uchar z = seq1queue.fromEnd(seqLoadLen);
if (z >= 4) {
isDna = false;
=====================================
src/GappedXdropAlignerPssm.cc
=====================================
@@ -45,8 +45,8 @@ int GappedXdropAligner::alignPssm(BigPtr seq,
for (int i = 0; i < simdLen; ++i) {
uchar x = *seq;
- seq1queue.push(x, i);
seq += seqIncrement * !isDelimiter(x, vectorOfMatchScores);
+ seq1queue.push(x, i);
pssmQueue.push(vectorOfMatchScores, i);
}
@@ -152,8 +152,8 @@ int GappedXdropAligner::alignPssm(BigPtr seq,
++numCells;
++seq1end;
uchar x = *seq;
- seq1queue.push(x, n + simdLen);
seq += seqIncrement * !isDelimiter(x, vectorOfMatchScores);
+ seq1queue.push(x, n + simdLen);
isDelimiter1 = isDelimiter(seq1queue.fromEnd(simdLen),
vectorOfMatchScores);
}
=====================================
src/makefile
=====================================
@@ -95,7 +95,7 @@ ScoreMatrixData.hh: ../data/*.mat
../build/mat-inc.sh ../data/*.mat > $@
VERSION1 = git describe --dirty
-VERSION2 = echo ' (HEAD -> main, tag: 1642) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
+VERSION2 = echo ' (HEAD -> main, tag: 1645) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
VERSION = \"`test -e ../.git && $(VERSION1) || $(VERSION2)`\"
=====================================
src/mcf_big_seq.hh
=====================================
@@ -35,11 +35,15 @@ struct BigPtr {
}
int operator*() const {
- return is4bit ? BigSeq::from4bit(beg, pos) : beg[pos];
+ return is4bit ? BigSeq::from4bit(beg, pos) : *beg;
}
BigPtr &operator+=(int i) {
- pos += i;
+ if (is4bit) {
+ pos += i;
+ } else {
+ beg += i;
+ }
return *this;
}
};
=====================================
src/split/cbrc_split_aligner.cc
=====================================
@@ -1146,12 +1146,12 @@ void SplitAligner::initMatricesForOneQuery(const SplitAlignerParams ¶ms,
for (unsigned i = 0; i < numAlns; ++i) initSpliceCoords(i);
}
- if (params.isGenome()) {
- spliceBegScores = params.spliceBegScores;
- spliceEndScores = params.spliceEndScores;
- spliceBegProbs = params.spliceBegProbs;
- spliceEndProbs = params.spliceEndProbs;
+ spliceBegScores = params.spliceBegScores;
+ spliceEndScores = params.spliceEndScores;
+ spliceBegProbs = params.spliceBegProbs;
+ spliceEndProbs = params.spliceEndProbs;
+ if (params.isGenome()) {
resizeMatrix(spliceBegSignals);
resizeMatrix(spliceEndSignals);
for (unsigned i = 0; i < numAlns; ++i) initSpliceSignals(params, i);
=====================================
test/maf-convert-test.out
=====================================
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chain 133 chr19 59128983 + 9629868 9629939 SRR359290.9030 75 + 4 75 149
71
+
chain 190 chr14 107349540 + 19585785 19585852 SRR359290.9030 75 + 8 75 150
67
+
chain 142 chr3 198022430 + 12112735 12112791 SRR359290.9030 75 + 19 75 151
56
+
chain 163 chr1 249250621 + 104113167 104113223 SRR359290.9030 75 + 19 75 152
56
+
chain 166 chr20 63025520 + 1142213 1142269 SRR359290.9030 75 + 19 75 153
56
+
chain 127 chr5 180915260 + 97675418 97675467 SRR359290.9030 75 + 26 75 154
49
+
chain 190 chr14 107349540 + 19987783 19987850 SRR359290.9030 75 - 0 67 155
67
+
chain 190 chr22 51304566 + 16255421 16255488 SRR359290.9030 75 - 0 67 156
67
+
chain 181 chr11 135006516 + 1824191 1824261 SRR359290.9030 75 - 0 70 157
70
+
chain 220 chr2 243199373 + 130831889 130831961 SRR359290.9030 75 - 0 72 158
72
+
chain 220 chr2 243199373 + 131220461 131220533 SRR359290.9030 75 - 0 72 159
72
+
chain 175 chr17 81195210 + 79477788 79477861 SRR359290.9030 75 - 0 73 160
73
+
chain 178 chr1 249250621 + 229567318 229567391 SRR359290.9030 75 - 0 73 161
73
+
chain 322 chr7 159138663 + 5567451 5567524 SRR359290.9030 75 - 0 73 162
73
+
chain 163 chr6 171115067 + 88985673 88985748 SRR359290.9030 75 - 0 75 163
75
+
chain 184 chr1 249250621 + 92694642 92694717 SRR359290.9030 75 - 0 75 164
75
+
chain 232 chr15 102531392 + 44281331 44281406 SRR359290.9030 75 - 0 75 165
75
+
chain 238 chr5 180915260 + 79595569 79595644 SRR359290.9030 75 - 0 75 166
75
+
chain 256 chr1 249250621 + 224051503 224051578 SRR359290.9030 75 - 0 75 167
75
+
chain 283 chr22 51304566 + 41470237 41470312 SRR359290.9030 75 - 0 75 168
75
+
chain 208 chr3 198022430 + 175695364 175695426 SRR359290.9030 75 - 12 75 169
44 0 1
18
+
chain 126 chr2 243199373 + 201864995 201865020 SRR359290.9030 75 - 41 66 170
25
+
chain 120 chrX 155270560 + 46147573 46147593 SRR359290.9030 75 - 55 75 171
20
+
chain 162 chr10 135534747 + 14542767 14542798 SRR359290.9033 75 + 0 31 172
31
+
chain 174 chr2 243199373 + 20176851 20176884 SRR359290.9033 75 + 0 33 173
33
+
chain 186 chr14 107349540 + 58238570 58238605 SRR359290.9033 75 + 0 35 174
35
+
chain 186 chr7 159138663 + 27338443 27338478 SRR359290.9033 75 + 0 35 175
35
+
chain 186 chrX 155270560 + 132396616 132396651 SRR359290.9033 75 + 0 35 176
35
+
chain 210 chr2 243199373 + 182832700 182832735 SRR359290.9033 75 + 0 35 177
35
+
chain 210 chr6 171115067 + 134665915 134665950 SRR359290.9033 75 + 0 35 178
35
+
chain 210 chr8 146364022 + 95914071 95914106 SRR359290.9033 75 + 0 35 179
35
+
chain 192 chr14 107349540 + 66369309 66369349 SRR359290.9033 75 + 0 40 180
40
+
chain 192 chr21 48129895 + 34998523 34998563 SRR359290.9033 75 + 0 40 181
40
+
chain 216 chr15 102531392 + 80896195 80896235 SRR359290.9033 75 + 0 40 182
40
+
chain 126 chr15 102531392 + 57301567 57301608 SRR359290.9033 75 + 0 41 183
41
+
chain 174 chr16 90354753 + 66908978 66909019 SRR359290.9033 75 + 0 41 184
41
+
chain 174 chr7 159138663 + 124124387 124124428 SRR359290.9033 75 + 0 41 185
41
+
chain 198 chr15 102531392 + 90230412 90230453 SRR359290.9033 75 + 0 41 186
41
+
chain 198 chr6 171115067 + 29604559 29604600 SRR359290.9033 75 + 0 41 187
41
+
chain 198 chr6_apd_hap1 4622290 + 908089 908130 SRR359290.9033 75 + 0 41 188
41
+
chain 198 chr6_cox_hap2 4795371 + 1123364 1123405 SRR359290.9033 75 + 0 41 189
41
+
chain 198 chr6_dbb_hap3 4610396 + 907914 907955 SRR359290.9033 75 + 0 41 190
41
+
chain 198 chr6_mann_hap4 4683263 + 907524 907565 SRR359290.9033 75 + 0 41 191
41
+
chain 198 chr6_mcf_hap5 4833398 + 907755 907796 SRR359290.9033 75 + 0 41 192
41
+
chain 198 chr6_qbl_hap6 4611984 + 907880 907921 SRR359290.9033 75 + 0 41 193
41
+
chain 198 chr6_ssto_hap7 4928567 + 945117 945158 SRR359290.9033 75 + 0 41 194
41
+
##gff-version 3
chr3 maf-convert match 23607557 23607579 138 + . Target=102 674 696;Name=102:674-696
chr14 maf-convert match 104715673 104715703 126 + . Target=102 480 508;Name=102:480-508
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/compare/4a4adfbde8e64494d652268e9e8715175e01a762...327077690d55ef7e386db223fb7f41012fa231d3
--
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/compare/4a4adfbde8e64494d652268e9e8715175e01a762...327077690d55ef7e386db223fb7f41012fa231d3
You're receiving this email because of your account on salsa.debian.org.
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