[med-svn] [Git][med-team/kma][master] 6 commits: routine-update: New upstream version
Lance Lin (@linqigang)
gitlab at salsa.debian.org
Thu Jan 12 14:54:07 GMT 2023
Lance Lin pushed to branch master at Debian Med / kma
Commits:
31ce0d77 by Lance Lin at 2023-01-12T21:14:33+07:00
routine-update: New upstream version
- - - - -
b4956cdf by Lance Lin at 2023-01-12T21:14:42+07:00
New upstream version 1.4.10
- - - - -
2b2928ec by Lance Lin at 2023-01-12T21:14:42+07:00
Update upstream source from tag 'upstream/1.4.10'
Update to upstream version '1.4.10'
with Debian dir 14e32467fbd35c9288ac7a4828160b3aa056ea7d
- - - - -
457a6c53 by Lance Lin at 2023-01-12T21:14:42+07:00
routine-update: Standards-Version: 4.6.2
- - - - -
18a077b5 by Lance Lin at 2023-01-12T21:15:30+07:00
routine-update: Ready to upload to unstable
- - - - -
8abb01c8 by Lance Lin at 2023-01-12T21:50:41+07:00
Update to new upstream version 1.4.10
- - - - -
8 changed files:
- compress.c
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/blhc.patch
- debian/upstream/metadata
- dist.c
- version.h
Changes:
=====================================
compress.c
=====================================
@@ -659,7 +659,7 @@ HashMapKMA * compressKMA_megaDB(HashMap *templates, FILE *out) {
fprintf(stderr, "# Calculating relative indexes.\n");
null_index = finalDB->n;
v_index = 0;
- while(templates->values[v_index] != 0) {
+ while(v_index != finalDB->size && templates->values[v_index] != 0) {
finalDB->exist[v_index] = v_index;
++v_index;
}
@@ -673,6 +673,7 @@ HashMapKMA * compressKMA_megaDB(HashMap *templates, FILE *out) {
finalDB->exist[i] = null_index;
}
}
+
/* decrease size of values to what is actually used */
templates->values = realloc(templates->values, templates->n * sizeof(unsigned *));
if(!templates->values) {
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+kma (1.4.10-1) unstable; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * Standards-Version: 4.6.2 (routine-update)
+ * d/copyright: Update debian copyright year to 2023
+ * d/patches/blhc.patch: Add Forwarded field
+ * d/upstream/metadata: Add Bug-Database and Bug-Submit fields
+
+ -- Lance Lin <lq27267 at gmail.com> Thu, 12 Jan 2023 21:15:30 +0700
+
kma (1.4.8-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -5,7 +5,7 @@ Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
zlib1g-dev
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
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/copyright
=====================================
@@ -8,7 +8,7 @@ Copyright: 2015-2017, Philip Clausen, Technical University of Denmark
License: Apache-2.0
Files: debian/*
-Copyright: 2018 Andreas Tille <tille at debian.org>
+Copyright: 2023 Andreas Tille <tille at debian.org>
License: Apache-2.0
License: Apache-2.0
=====================================
debian/patches/blhc.patch
=====================================
@@ -1,5 +1,6 @@
Description: Propagate CPPFLAGS into Makefile
Author: Nilesh Patra <nilesh at debian.org>
+Forwarded: yes
Last-Update: 2021-04-14
--- a/Makefile
+++ b/Makefile
=====================================
debian/upstream/metadata
=====================================
@@ -20,3 +20,6 @@ Registry:
- Name: conda:bioconda
Entry: kma
Repository: https://bitbucket.org/genomicepidemiology/kma
+Bug-Database: https://bitbucket.org/genomicepidemiology/kma/issues?status=new&status=open
+Bug-Submit: https://bitbucket.org/genomicepidemiology/kma/issues/new
+
=====================================
dist.c
=====================================
@@ -19,6 +19,7 @@
#define _XOPEN_SOURCE 600
#include <limits.h>
+#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
@@ -318,7 +319,8 @@ void kmerSimilarity_thread(HashMapKMA *DB, Matrix *Dist, int *N, int thread_num,
}
int kmerDist(int Ni, int Nj, int D) {
- return Ni + Nj - (D << 1);
+ D = Ni + Nj - (D << 1);
+ return (D < 0) ? 0 : D;
}
int kmerShared(int Ni, int Nj, int D) {
@@ -326,8 +328,9 @@ int kmerShared(int Ni, int Nj, int D) {
}
int chi2dist(int Ni, int Nj, int D) {
- D = (Ni + Nj - (D << 1));
- return D * D / (Ni + Nj);
+ long d = (Ni + Nj - (D << 1));
+ d = d * d / (Ni + Nj);
+ return (d < 0) ? 0 : d;
}
void printIntLtdPhy(char *outfile, Matrix *Dist, int *N, FILE *name_file, Qseqs *template_name, unsigned format, int thread_num, volatile int *lock, const char *method, int (*distPtr)(int, int, int)) {
@@ -336,7 +339,7 @@ void printIntLtdPhy(char *outfile, Matrix *Dist, int *N, FILE *name_file, Qseqs
static int next_i, next_j, entrance = 0;
static long unsigned row_bias = 0;
volatile int *thread_wait;
- int i, j, j_end, chunk, N_i, *Nj, **D, *Di;
+ int i, j, j_end, d, chunk, N_i, *Nj, **D, *Di;
char *outfile_chunk, *name;
/* init */
@@ -402,7 +405,8 @@ void printIntLtdPhy(char *outfile, Matrix *Dist, int *N, FILE *name_file, Qseqs
Di = D[i] + --j;
Nj = N + j;
while(++j < j_end) {
- outfile_chunk += sprintf(outfile_chunk, "\t%10d", distPtr(N_i, *++Nj, *++Di));
+ d = distPtr(N_i, *++Nj, *++Di);
+ outfile_chunk += sprintf(outfile_chunk, "\t%10d", (d < 0 ? 0 : d));
}
/* fix null character */
*outfile_chunk = (j == i) ? '\n' : '\t';
@@ -422,43 +426,53 @@ void printIntLtdPhy(char *outfile, Matrix *Dist, int *N, FILE *name_file, Qseqs
}
double kmerQuery(int Ni, int Nj, int D) {
- return 100.0 * D / Ni;
+ double d = 100.0 * D / Ni;
+ return (d < 0) ? 0.0 : ((100 < d) ? 100.0 : d);
}
double kmerTemplate(int Ni, int Nj, int D) {
- return 100.0 * D / Nj;
+ double d = 100.0 * D / Nj;
+ return (d < 0) ? 0.0 : ((100 < d) ? 100.0 : d);
}
double kmerAvg(int Ni, int Nj, int D) {
- return 200.0 * D / (Ni + Nj);
+ double d = 200.0 * D / (Ni + Nj);
+ return (d < 0) ? 0.0 : ((100 < d) ? 100.0 : d);
}
double kmerInvAvg(int Ni, int Nj, int D) {
- return 100.0 - 200.0 * D / (Ni + Nj);
+ double d = 100.0 - 200.0 * D / (Ni + Nj);
+ return (d < 0) ? 0.0 : ((100 < d) ? 100.0 : d);
}
double kmerJaccardDist(int Ni, int Nj, int D) {
- return 1.0 - (double)(D) / (Ni + Nj - D);
+ double d = 1.0 - (double)(D) / (Ni + Nj - D);
+ return (d < 0) ? 0.0 : ((1 < d) ? 1.0 : d);
}
double kmerJaccardSim(int Ni, int Nj, int D) {
- return (double)(D) / (Ni + Nj - D);
+ double d = (double)(D) / (Ni + Nj - D);
+ return (d < 0) ? 0.0 : ((1 < d) ? 1.0 : d);
}
double kmerCosineDist(int Ni, int Nj, int D) {
- return 1.0 - (double)(D) / (Ni + Nj);
+ double d = 1.0 - (double)(D) / (sqrt(Ni) * sqrt(Nj));
+ return (d < 0) ? 0.0 : ((1 < d) ? 1.0 : d);
}
double kmerCosineSim(int Ni, int Nj, int D) {
- return (double)(D) / (Ni + Nj);
+ double d = (double)(D) / (sqrt(Ni) * sqrt(Nj));
+ return (d < 0) ? 0.0 : ((1 < d) ? 1.0 : d);
}
double kmerOverlapCoef(int Ni, int Nj, int D) {
- return (double)(D) / (Ni < Nj ? Ni : Nj);
+ double d = (double)(D) / (Ni < Nj ? Ni : Nj);
+ return (d < 0) ? 0.0 : ((1 < d) ? 1.0 : d);
}
double kmerInvOverlapCoef(int Ni, int Nj, int D) {
- return 1.0 - (double)(D) / (Ni < Nj ? Ni : Nj);
+ double d = 1.0 - (double)(D) / (Ni < Nj ? Ni : Nj);
+ return (d < 0) ? 0.0 : ((1 < d) ? 1.0 : d);
}
void printDoublePhy(char *outfile, Matrix *Dist, int *N, FILE *name_file, Qseqs *template_name, unsigned format, const char *formatString, int ltd, int thread_num, volatile int *lock, const char *method, double (*distPtr)(int, int, int)) {
@@ -469,6 +483,7 @@ void printDoublePhy(char *outfile, Matrix *Dist, int *N, FILE *name_file, Qseqs
volatile int *thread_wait;
int i, j, j_end, chunk, N_i, *Nj, **D, *Di;
char endChar, *outfile_chunk, *name;
+ double d;
/* init */
D = Dist->mat;
@@ -541,18 +556,22 @@ void printDoublePhy(char *outfile, Matrix *Dist, int *N, FILE *name_file, Qseqs
if(j_end < i) {
while(++j < j_end) {
- outfile_chunk += sprintf(outfile_chunk, formatString, distPtr(N_i, *++Nj, *++Di));
+ d = distPtr(N_i, *++Nj, *++Di);
+ outfile_chunk += sprintf(outfile_chunk, formatString, (d < 0 ? 0 : d));
}
} else if(i < j) {
while(++j < j_end) {
- outfile_chunk += sprintf(outfile_chunk, formatString, distPtr(N_i, *++Nj, D[j][i]));
+ d = distPtr(N_i, *++Nj, D[j][i]);
+ outfile_chunk += sprintf(outfile_chunk, formatString, (d < 0 ? 0 : d));
}
} else {
while(++j < j_end) {
if(j < i) {
- outfile_chunk += sprintf(outfile_chunk, formatString, distPtr(N_i, *++Nj, *++Di));
+ d = distPtr(N_i, *++Nj, *++Di);
+ outfile_chunk += sprintf(outfile_chunk, formatString, (d < 0 ? 0 : d));
} else if(i < j) {
- outfile_chunk += sprintf(outfile_chunk, formatString, distPtr(N_i, *++Nj, D[j][i]));
+ d = distPtr(N_i, *++Nj, D[j][i]);
+ outfile_chunk += sprintf(outfile_chunk, formatString, (d < 0 ? 0 : d));
} else {
outfile_chunk += sprintf(outfile_chunk, formatString, 100.0);
++Nj;
@@ -944,7 +963,7 @@ int dist_main(int argc, char *argv[]) {
fprintf(stdout, "#%9d\t%s\n", 256, "Cosine distance");
fprintf(stdout, "#%9d\t%s\n", 512, "Cosine similarity");
fprintf(stdout, "#%9d\t%s\n", 1024, "Szymkiewicz–Simpson similarity");
- fprintf(stdout, "#%9d\t%s\n", 2048, "Szymkiewicz–Simpson distance");
+ fprintf(stdout, "#%9d\t%s\n", 2048, "Szymkiewicz–Simpson dissimilarity");
fprintf(stdout, "#%9d\t%s\n", 4096, "Chi-square distance");
fprintf(stdout, "#\n");
return 0;
=====================================
version.h
=====================================
@@ -17,4 +17,4 @@
* limitations under the License.
*/
-#define KMA_VERSION "1.4.8"
+#define KMA_VERSION "1.4.10"
View it on GitLab: https://salsa.debian.org/med-team/kma/-/compare/db6e46023ae878261b9d66dbb493ea2cbb75b94c...8abb01c868a622ecb0d2d76987350483a62fcfe6
--
View it on GitLab: https://salsa.debian.org/med-team/kma/-/compare/db6e46023ae878261b9d66dbb493ea2cbb75b94c...8abb01c868a622ecb0d2d76987350483a62fcfe6
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