[med-svn] [Git][med-team/kma][upstream] New upstream version 1.3.23

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch upstream at Debian Med / kma


Commits:
3bccb965 by Nilesh Patra at 2021-07-16T22:39:56+05:30
New upstream version 1.3.23
- - - - -


7 changed files:

- compdna.c
- compdna.h
- 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);


=====================================
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/-/commit/3bccb96579626644df04d9d9ff949b85b8029800

-- 
View it on GitLab: https://salsa.debian.org/med-team/kma/-/commit/3bccb96579626644df04d9d9ff949b85b8029800
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