[med-svn] [Git][med-team/kma][master] 5 commits: New upstream version 1.4.21
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Wed Mar 5 12:50:21 GMT 2025
Étienne Mollier pushed to branch master at Debian Med / kma
Commits:
9c6d1efa by Étienne Mollier at 2025-03-05T13:43:42+01:00
New upstream version 1.4.21
- - - - -
1e104e3a by Étienne Mollier at 2025-03-05T13:43:42+01:00
Update upstream source from tag 'upstream/1.4.21'
Update to upstream version '1.4.21'
with Debian dir da20754f7f23b305e089747dad14990d49539b4d
- - - - -
ca89b93a by Étienne Mollier at 2025-03-05T13:44:15+01:00
d/control: declare compliance to standards version 4.7.2.
- - - - -
504f8615 by Étienne Mollier at 2025-03-05T13:45:57+01:00
typos.patch: delete: applied upstream.
- - - - -
02d24d58 by Étienne Mollier at 2025-03-05T13:47:47+01:00
d/changelog: ready for upload to unstable.
- - - - -
9 changed files:
- assembly.c
- debian/changelog
- debian/control
- debian/patches/series
- − debian/patches/typos.patch
- index.c
- kma.c
- update.c
- version.h
Changes:
=====================================
assembly.c
=====================================
@@ -517,9 +517,7 @@ void * assemble_KMA_threaded(void *arg) {
for(j = 0; j < 6; ++j) {
myBias += assembly[pos].counts[j];
}
- if(myBias > 0) { /* here */ /* not here */ /* why subtract one */ /* and check prior to insertion, for which -- is appropiate */
- --myBias;
- }
+
/* find position of insertion */
gaps = pos;
if(pos != 0) {
@@ -1320,7 +1318,7 @@ void alnToMat(AssemInfo *matrix, Assem *aligned_assem, Aln *aligned, AlnScore al
static volatile int Lock = 0;
volatile int *excludeMatrix = &Lock;
- int i, pos, aln_len, start, read_score, myBias, gaps;
+ int i, pos, aln_len, start, read_score, myBias, tmp, gaps;
short unsigned *counts;
Assembly *assembly;
@@ -1339,8 +1337,23 @@ void alnToMat(AssemInfo *matrix, Assem *aligned_assem, Aln *aligned, AlnScore al
}
++aligned_assem->readCountAln;
- /* diff */
+ /* trim trailing gaps */
+ i = aln_len - 1;
+ while(i && (aligned->t[i] == 5 || aligned->q[i] == 5)) {
+ --i;
+ }
+ aln_len = i + 1;
+
+ /* trim leading gaps */
i = 0;
+ while(i < aln_len && (aligned->t[i] == 5 || aligned->q[i] == 5)) {
+ if(aligned->q[i] == 5) {
+ ++start;
+ }
+ ++i;
+ }
+
+ /* diff */
pos = start;
assembly = matrix->assmb;
while(i < aln_len) {
@@ -1356,20 +1369,29 @@ void alnToMat(AssemInfo *matrix, Assem *aligned_assem, Aln *aligned, AlnScore al
gaps = pos;
pos = pos ? (pos - 1) : (t_len - 1);
- /* find position of insertion, it it already exists */
+ /* find position of insertion, if it already exists */
while(assembly[pos].next != gaps) {
pos = assembly[pos].next;
}
/* get number of bases not supporting the insertion */
counts = assembly[pos].counts;
- myBias = counts[0] + counts[1] + counts[2] + counts[3] + counts[4] + counts[5] - 1;
+ myBias = *counts;
+ myBias += *++counts;
+ myBias += *++counts;
+ myBias += *++counts;
+ myBias += *++counts;
+ myBias += *++counts;
/* get minimum of bases sorrounding new insertion */
counts = assembly[gaps].counts;
- if((counts[0] + counts[1] + counts[2] + counts[3] + counts[4] + counts[5]) < myBias) {
- myBias = counts[0] + counts[1] + counts[2] + counts[3] + counts[4] + counts[5];
- }
+ tmp = *counts;
+ tmp += *++counts;
+ tmp += *++counts;
+ tmp += *++counts;
+ tmp += *++counts;
+ tmp += *++counts;
+ myBias = (tmp < myBias) ? tmp : (myBias - 1);
if(USHRT_MAX < myBias) {
myBias = USHRT_MAX;
}
@@ -1443,15 +1465,33 @@ void alnToMatDense(AssemInfo *matrix, Assem *aligned_assem, Aln *aligned, AlnSco
}
++aligned_assem->readCountAln;
+ /* trim trailing gaps */
+ i = aln_len - 1;
+ while(i < aln_len && (aligned->t[i] == 5 || aligned->q[i] == 5)) {
+ --i;
+ }
+ aln_len = i + 1;
+
+ /* trim leading gaps */
+ i = 0;
+ while(i && (aligned->t[i] == 5 || aligned->q[i] == 5)) {
+ if(aligned->q[i] == 5) {
+ ++start;
+ }
+ ++i;
+ }
+
/* diff */
+ pos = start;
assembly = matrix->assmb;
- for(i = 0, pos = start; i < aln_len; ++i) {
+ while(i < aln_len) {
if(aligned->t[i] != 5) {
if(!++assembly[pos].counts[aligned->q[i]]) {
assembly[pos].counts[aligned->q[i]] = USHRT_MAX;
}
pos = assembly[pos].next;
}
+ ++i;
}
unlock(excludeMatrix);
}
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+kma (1.4.21-1) unstable; urgency=medium
+
+ * New upstream version 1.4.21
+ * d/control: declare compliance to standards version 4.7.2.
+ * typos.patch: delete: applied upstream.
+
+ -- Étienne Mollier <emollier at debian.org> Wed, 05 Mar 2025 13:46:24 +0100
+
kma (1.4.19-1) unstable; urgency=medium
* New upstream version 1.4.19
=====================================
debian/control
=====================================
@@ -7,7 +7,7 @@ Priority: optional
Build-Depends: debhelper-compat (= 13),
architecture-is-64-bit,
zlib1g-dev
-Standards-Version: 4.7.1
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/kma
Vcs-Git: https://salsa.debian.org/med-team/kma.git
Homepage: https://bitbucket.org/genomicepidemiology/kma
=====================================
debian/patches/series
=====================================
@@ -1,2 +1 @@
blhc.patch
-typos.patch
=====================================
debian/patches/typos.patch deleted
=====================================
@@ -1,39 +0,0 @@
-Description: fix typos caught by lintian.
-Author: Étienne Mollier <emollier at debian.org>
-Forwarded: https://bitbucket.org/genomicepidemiology/kma/issues/92/typos-caught-by-lintian
-Last-Update: 2025-02-26
----
-This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
---- kma.orig/index.c
-+++ kma/index.c
-@@ -676,7 +676,7 @@
- /* decontaminate */
- if(deconcount != 0) {
- /* open values */
-- fprintf(stderr, "# Openning values\n");
-+ fprintf(stderr, "# Opening values\n");
- if(!finalDB) {
- strcat(outputfilename, ".comp.b");
- out = sfopen(outputfilename, "rb");
---- kma.orig/kma.c
-+++ kma/kma.c
-@@ -164,7 +164,7 @@
- fprintf(out, "# %16s\t%-32s\t%s\n", "-1t1", "One query to one template", "False");
- fprintf(out, "# %16s\t%-32s\t%s\n", "-hmm", "Use a HMM to assign template(s)", "False");
- fprintf(out, "# %16s\t%-32s\t%s\n", "-ck", "Count k-mers over pseudo alignment", "False");
-- fprintf(out, "# %16s\t%-32s\t%s\n", "-localopen", "Penalty for openning a local chain", "6");
-+ fprintf(out, "# %16s\t%-32s\t%s\n", "-localopen", "Penalty for opening a local chain", "6");
- fprintf(out, "# %16s\t%-32s\t%s\n", "-mct", "Max overlap between templates", "0.1");
- fprintf(out, "# %16s\t%-32s\t%s\n", "-lc", "Length corrected template chaining", "False");
-
---- kma.orig/update.c
-+++ kma/update.c
-@@ -238,7 +238,7 @@
- } else {
- helpOut = stderr;
- }
-- fprintf(helpOut, "# KMA_update syncronises kma-indexes to the needed version.\n");
-+ fprintf(helpOut, "# KMA_update synchronises kma-indexes to the needed version.\n");
- fprintf(helpOut, "# Options are:\t\tDesc:\t\t\t\t\tRequirements:\n");
- fprintf(helpOut, "#\n");
- fprintf(helpOut, "#\t-t_db\t\tTemplate DB\t\t\t\tREQUIRED\n");
=====================================
index.c
=====================================
@@ -676,7 +676,7 @@ int index_main(int argc, char *argv[]) {
/* decontaminate */
if(deconcount != 0) {
/* open values */
- fprintf(stderr, "# Openning values\n");
+ fprintf(stderr, "# Opening values\n");
if(!finalDB) {
strcat(outputfilename, ".comp.b");
out = sfopen(outputfilename, "rb");
=====================================
kma.c
=====================================
@@ -164,7 +164,7 @@ static void helpMessage(int exitStatus) {
fprintf(out, "# %16s\t%-32s\t%s\n", "-1t1", "One query to one template", "False");
fprintf(out, "# %16s\t%-32s\t%s\n", "-hmm", "Use a HMM to assign template(s)", "False");
fprintf(out, "# %16s\t%-32s\t%s\n", "-ck", "Count k-mers over pseudo alignment", "False");
- fprintf(out, "# %16s\t%-32s\t%s\n", "-localopen", "Penalty for openning a local chain", "6");
+ fprintf(out, "# %16s\t%-32s\t%s\n", "-localopen", "Penalty for opening a local chain", "6");
fprintf(out, "# %16s\t%-32s\t%s\n", "-mct", "Max overlap between templates", "0.1");
fprintf(out, "# %16s\t%-32s\t%s\n", "-lc", "Length corrected template chaining", "False");
=====================================
update.c
=====================================
@@ -238,7 +238,7 @@ static void helpMessage(int exeStatus) {
} else {
helpOut = stderr;
}
- fprintf(helpOut, "# KMA_update syncronises kma-indexes to the needed version.\n");
+ fprintf(helpOut, "# KMA_update synchronises kma-indexes to the needed version.\n");
fprintf(helpOut, "# Options are:\t\tDesc:\t\t\t\t\tRequirements:\n");
fprintf(helpOut, "#\n");
fprintf(helpOut, "#\t-t_db\t\tTemplate DB\t\t\t\tREQUIRED\n");
=====================================
version.h
=====================================
@@ -17,4 +17,4 @@
* limitations under the License.
*/
-#define KMA_VERSION "1.4.19"
+#define KMA_VERSION "1.4.21"
View it on GitLab: https://salsa.debian.org/med-team/kma/-/compare/242c7aef74ffabba4b576e619b344a080248f674...02d24d580eb6a217aee7d09f2b349f28bec1cfac
--
View it on GitLab: https://salsa.debian.org/med-team/kma/-/compare/242c7aef74ffabba4b576e619b344a080248f674...02d24d580eb6a217aee7d09f2b349f28bec1cfac
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