[med-svn] [Git][med-team/kma][master] 3 commits: New upstream version 1.3.23
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Fri Jul 16 18:16:41 BST 2021
Nilesh Patra pushed to branch master at Debian Med / kma
Commits:
ed0e67e5 by Nilesh Patra at 2021-07-16T17:16:10+00:00
New upstream version 1.3.23
- - - - -
1ec2ebe5 by Nilesh Patra at 2021-07-16T17:16:11+00:00
Update manpage
- - - - -
319fc038 by Nilesh Patra at 2021-07-16T17:16:11+00:00
Interim changelog entry
- - - - -
11 changed files:
- compdna.c
- compdna.h
- debian/changelog
- debian/kma.1
- debian/kma_index.1
- debian/kma_shm.1
- makeindex.c
- qseqs.c
- qseqs.h
- seqparse.c
- version.h
Changes:
=====================================
compdna.c
=====================================
@@ -24,7 +24,7 @@
#include "qseqs.h"
#include "stdnuc.h"
-void allocComp(CompDNA *compressor, int size) {
+void allocComp(CompDNA *compressor, unsigned size) {
compressor->seqlen = 0;
if(size & 31) {
=====================================
compdna.h
=====================================
@@ -22,16 +22,16 @@
#ifndef COMPDNA
typedef struct compDNA CompDNA;
struct compDNA {
- int seqlen;
- int size;
- int complen;
+ unsigned seqlen;
+ unsigned size;
+ unsigned complen;
long unsigned *seq;
int *N;
};
#define COMPDNA 1
#endif
-void allocComp(CompDNA *compressor, int size);
+void allocComp(CompDNA *compressor, unsigned size);
void freeComp(CompDNA *compressor);
CompDNA * setComp(unsigned size);
void destroyComp(CompDNA *src);
=====================================
debian/changelog
=====================================
@@ -1,6 +1,6 @@
-kma (1.3.22-1) UNRELEASED; urgency=medium
+kma (1.3.23-1) UNRELEASED; urgency=medium
- * New upstream version 1.3.22
+ * New upstream version 1.3.23
* d/*.1: Update Manpages
* d/p/blhc.patch: Propagate hardening flags to fix blhc
=====================================
debian/kma.1
=====================================
@@ -1,10 +1,10 @@
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
-.TH KMA "1" "June 2021" "kma 1.3.22" "User Commands"
+.TH KMA "1" "July 2021" "kma 1.3.23" "User Commands"
.SH NAME
kma \- maps and/or aligns raw reads to a template database
.SH DESCRIPTION
.IP
-KMA\-1.3.22 maps and/or aligns raw reads to a template database.
+KMA\-1.3.23 maps and/or aligns raw reads to a template database.
.TP
Options:
Desc: Default:
=====================================
debian/kma_index.1
=====================================
@@ -1,5 +1,5 @@
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
-.TH KMA_INDEX "1" "June 2021" "kma_index 1.3.22" "User Commands"
+.TH KMA_INDEX "1" "July 2021" "kma_index 1.3.23" "User Commands"
.SH NAME
kma_index \- creates the databases needed to run KMA, from a list of fasta files given
.SH DESCRIPTION
=====================================
debian/kma_shm.1
=====================================
@@ -1,5 +1,5 @@
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
-.TH KMA_SHM "1" "June 2021" "kma_shm 1.3.22" "User Commands"
+.TH KMA_SHM "1" "July 2021" "kma_shm 1.3.23" "User Commands"
.SH NAME
kma_shm \- sets up a shared database (sysV) for mapping with KMA
.SH DESCRIPTION
=====================================
makeindex.c
=====================================
@@ -95,7 +95,7 @@ void makeDB(HashMap *templates, int kmerindex, char **inputfiles, int fileCount,
while(FileBuffgetFsa(inputfile, header, qseq, trans)) {
if(qseq->len >= compressor->size) {
freeComp(compressor);
- allocComp(compressor, qseq->len << 1);
+ allocComp(compressor, qseq->size);
}
bias = compDNAref(compressor, qseq->seq, qseq->len);
=====================================
qseqs.c
=====================================
@@ -21,7 +21,7 @@
#include "pherror.h"
#include "qseqs.h"
-Qseqs * setQseqs(int size) {
+Qseqs * setQseqs(unsigned size) {
Qseqs *dest;
=====================================
qseqs.h
=====================================
@@ -20,15 +20,15 @@
#ifndef QSEQS
typedef struct qseqs Qseqs;
struct qseqs {
- int size;
- int len;
+ unsigned size;
+ unsigned len;
unsigned char *seq;
};
#define QSEQS 1
#endif
/* initialize Qseqs */
-Qseqs * setQseqs(int size);
+Qseqs * setQseqs(unsigned size);
/* destroy Qseqs */
void destroyQseqs(Qseqs *dest);
void insertKmerBound(Qseqs *header, int start, int end);
=====================================
seqparse.c
=====================================
@@ -66,7 +66,7 @@ int openAndDetermine(FileBuff *inputfile, char *filename) {
int FileBuffgetFsa(FileBuff *src, Qseqs *header, Qseqs *qseq, char *trans) {
unsigned char *buff, *seq;
- int size, avail;
+ unsigned size, avail;
/* init */
avail = src->bytes;
@@ -161,7 +161,7 @@ int FileBuffgetFsa(FileBuff *src, Qseqs *header, Qseqs *qseq, char *trans) {
int FileBuffgetFsaSeq(FileBuff *src, Qseqs *qseq, char *trans) {
unsigned char *buff, *seq;
- int size, avail;
+ unsigned size, avail;
/* init */
avail = src->bytes;
@@ -241,7 +241,7 @@ int FileBuffgetFsaSeq(FileBuff *src, Qseqs *qseq, char *trans) {
int FileBuffgetFq(FileBuff *src, Qseqs *header, Qseqs *qseq, Qseqs *qual, char *trans) {
unsigned char *buff, *seq;
- int size, avail;
+ unsigned size, avail;
/* init */
avail = src->bytes;
@@ -396,7 +396,7 @@ int FileBuffgetFq(FileBuff *src, Qseqs *header, Qseqs *qseq, Qseqs *qual, char *
int FileBuffgetFqSeq(FileBuff *src, Qseqs *qseq, Qseqs *qual, char *trans) {
unsigned char *buff, *seq;
- int size, avail;
+ unsigned size, avail;
/* init */
avail = src->bytes;
=====================================
version.h
=====================================
@@ -17,4 +17,4 @@
* limitations under the License.
*/
-#define KMA_VERSION "1.3.22"
+#define KMA_VERSION "1.3.23"
View it on GitLab: https://salsa.debian.org/med-team/kma/-/compare/049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef...319fc038bff748bbc40f57e010f9fe2fa6adf4cc
--
View it on GitLab: https://salsa.debian.org/med-team/kma/-/compare/049fadc4b9b12b6ff575bd4bdfb0d7e6551dc3ef...319fc038bff748bbc40f57e010f9fe2fa6adf4cc
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