[med-svn] [Git][med-team/kma][upstream] New upstream version 1.4.8
Lance Lin (@linqigang)
gitlab at salsa.debian.org
Wed Nov 23 15:01:30 GMT 2022
Lance Lin pushed to branch upstream at Debian Med / kma
Commits:
9bfc7814 by Lance Lin at 2022-11-23T21:57:18+07:00
New upstream version 1.4.8
- - - - -
6 changed files:
- hashmapkma.c
- mt1.c
- runkma.c
- shm.c
- spltdb.c
- version.h
Changes:
=====================================
hashmapkma.c
=====================================
@@ -439,6 +439,10 @@ int hashMapKMA_load(HashMapKMA *dest, FILE *file, const char *filename) {
--dest->size;
}
+ if(seekSize) {
+ sfseek(file, seekSize, SEEK_CUR);
+ seekSize = 0;
+ }
if(fread(&dest->kmersize, sizeof(unsigned), 1, file)) {
sfread(&dest->flag, sizeof(unsigned), 1, file);
setCmerPointers(dest->flag);
@@ -454,7 +458,7 @@ void hashMapKMA_load_shm(HashMapKMA *dest, FILE *file, const char *filename) {
key_t key;
int shmid;
- long unsigned size;
+ long unsigned size, seekSize;
/* load sizes */
sfread(&dest->DB_size, sizeof(unsigned), 1, file);
@@ -491,6 +495,7 @@ void hashMapKMA_load_shm(HashMapKMA *dest, FILE *file, const char *filename) {
}
key = ftok(filename, 'e');
shmid = shmget(key, size, 0666);
+ seekSize = size;
if(shmid < 0) {
/* not shared */
fprintf(stderr, "DB e not shared, see kma_shm\n");
@@ -514,6 +519,7 @@ void hashMapKMA_load_shm(HashMapKMA *dest, FILE *file, const char *filename) {
}
key = ftok(filename, 'v');
shmid = shmget(key, size, 0666);
+ seekSize += size;
if(shmid < 0) {
/* not shared */
fprintf(stderr, "DB v not shared, see kma_shm\n");
@@ -540,6 +546,7 @@ void hashMapKMA_load_shm(HashMapKMA *dest, FILE *file, const char *filename) {
}
key = ftok(filename, 'k');
shmid = shmget(key, size, 0666);
+ seekSize += size;
if(shmid < 0) {
/* not shared */
fprintf(stderr, "DB k not shared, see kma_shm\n");
@@ -561,6 +568,7 @@ void hashMapKMA_load_shm(HashMapKMA *dest, FILE *file, const char *filename) {
}
key = ftok(filename, 'i');
shmid = shmget(key, size, 0666);
+ seekSize += size;
if(shmid < 0) {
/* not shared */
fprintf(stderr, "DB i not shared, see kma_shm\n");
@@ -575,6 +583,10 @@ void hashMapKMA_load_shm(HashMapKMA *dest, FILE *file, const char *filename) {
--dest->size;
}
+ if(seekSize) {
+ sfseek(file, seekSize, SEEK_CUR);
+ seekSize = 0;
+ }
if(fread(&dest->kmersize, sizeof(unsigned), 1, file)) {
sfread(&dest->flag, sizeof(unsigned), 1, file);
setCmerPointers(dest->flag);
=====================================
mt1.c
=====================================
@@ -433,7 +433,7 @@ void runKMA_Mt1(char *templatefilename, char *outputfilename, char *exePrev, int
}
if(ID_t <= id && 0 < id && Depth_t <= depth) {
/* Output result */
- fprintf(res_out, "%-12s\t%8lu\t%8d\t%8d\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%4.1e\n",
+ fprintf(res_out, "%s\t%8lu\t%8d\t%8d\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%4.1e\n",
thread->template_name, read_score, 0, t_len, id, cover, q_id, q_cover, (double) depth, (double) read_score, p_value);
if(tsv) {
printsv(tsv_out, tsv, thread->template_name, aligned_assem, t_len, aligned_assem->readCountAln, read_score, 0, (double) read_score, p_value, read_score);
@@ -452,7 +452,7 @@ void runKMA_Mt1(char *templatefilename, char *outputfilename, char *exePrev, int
/* destroy this DB index */
hashMapCCI_destroy(template_index);
} else if(ID_t == 0.0) {
- fprintf(res_out, "%-12s\t%8ld\t%8u\t%8d\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%4.1e\n",
+ fprintf(res_out, "%s\t%8ld\t%8u\t%8d\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%4.1e\n",
thread->template_name, read_score, 0, t_len, 0.0, 0.0, 0.0, 0.0, (double) depth, (double) read_score, p_value);
if(tsv) {
printsv(tsv_out, tsv, thread->template_name, aligned_assem, t_len, aligned_assem->readCountAln, read_score, 0, (double) read_score, p_value, read_score);
=====================================
runkma.c
=====================================
@@ -781,8 +781,7 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC
if(ID_t <= id && 0 < id && Depth_t <= depth) {
/* Output result */
- fprintf(res_out, "%-12s\t%8ld\t%8u\t%8d\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%4.1e\n",
- thread->template_name, read_score, (unsigned) expected, t_len, id, cover, q_id, q_cover, (double) depth, (double) q_value, p_value);
+ fprintf(res_out, "%s\t%8ld\t%8u\t%8d\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%4.1e\n", thread->template_name, read_score, (unsigned) expected, t_len, id, cover, q_id, q_cover, (double) depth, (double) q_value, p_value);
if(tsv) {
printsv(tsv_out, tsv, thread->template_name, aligned_assem, t_len, readCounts[template], read_score, expected, q_value, p_value, alignment_scores[template]);
}
@@ -813,8 +812,7 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC
aln_len = aligned_assem->aln_len;
cover = 100.0 * aln_len / t_len;
q_cover = 100.0 * t_len / aln_len;
- fprintf(res_out, "%-12s\t%8ld\t%8u\t%8d\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%4.1e\n",
- thread->template_name, read_score, (unsigned) expected, t_len, 0.0, cover, 0.0, q_cover, (double) depth, (double) q_value, p_value);
+ fprintf(res_out, "%s\t%8ld\t%8u\t%8d\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%4.1e\n", thread->template_name, read_score, (unsigned) expected, t_len, 0.0, cover, 0.0, q_cover, (double) depth, (double) q_value, p_value);
if(tsv) {
printsv(tsv_out, tsv, thread->template_name, aligned_assem, t_len, readCounts[template], read_score, expected, q_value, p_value, alignment_scores[template]);
}
@@ -1497,8 +1495,7 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int
}
if(ID_t <= id && Depth_t <= depth) {
/* Output result */
- fprintf(res_out, "%-12s\t%8ld\t%8u\t%8d\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%4.1e\n",
- thread->template_name, read_score, (unsigned) expected, t_len, id, cover, q_id, q_cover, (double) depth, (double) q_value, p_value);
+ fprintf(res_out, "%s\t%8ld\t%8u\t%8d\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%4.1e\n", thread->template_name, read_score, (unsigned) expected, t_len, id, cover, q_id, q_cover, (double) depth, (double) q_value, p_value);
if(tsv) {
printsv(tsv_out, tsv, thread->template_name, aligned_assem, t_len, readCounts[template], read_score, expected, q_value, p_value, alignment_scores[template]);
}
@@ -1534,8 +1531,7 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int
aln_len = aligned_assem->aln_len;
cover = 100.0 * aln_len / t_len;
q_cover = 0;
- fprintf(res_out, "%-12s\t%8ld\t%8u\t%8d\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%4.1e\n",
- thread->template_name, read_score, (unsigned) expected, t_len, 0.0, cover, 0.0, q_cover, (double) depth, (double) q_value, p_value);
+ fprintf(res_out, "%s\t%8ld\t%8u\t%8d\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%4.1e\n", thread->template_name, read_score, (unsigned) expected, t_len, 0.0, cover, 0.0, q_cover, (double) depth, (double) q_value, p_value);
if(tsv) {
printsv(tsv_out, tsv, thread->template_name, aligned_assem, t_len, readCounts[template], read_score, expected, q_value, p_value, alignment_scores[template]);
}
=====================================
shm.c
=====================================
@@ -209,6 +209,7 @@ void hashMapKMA_destroySHM(HashMapKMA *dest, FILE *file, const char *filename) {
shmid = shmget(key, size, 0666);
if(shmid >= 0) {
shmctl(shmid, IPC_RMID, NULL);
+ sfseek(file, size, SEEK_CUR);
}
/* values */
@@ -222,6 +223,7 @@ void hashMapKMA_destroySHM(HashMapKMA *dest, FILE *file, const char *filename) {
shmid = shmget(key, size, 0666);
if(shmid >= 0) {
shmctl(shmid, IPC_RMID, NULL);
+ sfseek(file, size, SEEK_CUR);
}
/* kmers */
@@ -235,6 +237,7 @@ void hashMapKMA_destroySHM(HashMapKMA *dest, FILE *file, const char *filename) {
shmid = shmget(key, size, 0666);
if(shmid >= 0) {
shmctl(shmid, IPC_RMID, NULL);
+ sfseek(file, size, SEEK_CUR);
}
/* value indexes */
@@ -248,6 +251,7 @@ void hashMapKMA_destroySHM(HashMapKMA *dest, FILE *file, const char *filename) {
shmid = shmget(key, size, 0666);
if(shmid >= 0) {
shmctl(shmid, IPC_RMID, NULL);
+ sfseek(file, size, SEEK_CUR);
}
if(fread(&dest->kmersize, sizeof(unsigned), 1, file)) {
=====================================
spltdb.c
=====================================
@@ -1199,7 +1199,7 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,
if(ID_t <= id && Depth_t <= depth) {
/* Output result */
- fprintf(res_out, "%-12s\t%8ld\t%8u\t%8d\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%4.1e\n",
+ fprintf(res_out, "%s\t%8ld\t%8u\t%8d\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%4.1e\n",
thread->template_name, read_score, (unsigned) expected, t_len, id, cover, q_id, q_cover, (double) depth, (double) q_value, p_value);
if(tsv) {
printsv(tsv_out, tsv, thread->template_name, aligned_assem, t_len, readCounts[template], read_score, expected, q_value, p_value, alignment_scores[template]);
@@ -1229,7 +1229,7 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,
if(ID_t == 0.0) {
depth = aligned_assem->depth;
depth /= t_len;
- fprintf(res_out, "%-12s\t%8ld\t%8u\t%8d\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%4.1e\n",
+ fprintf(res_out, "%s\t%8ld\t%8u\t%8d\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%8.2f\t%4.1e\n",
thread->template_name, read_score, (unsigned) expected, t_len, 0.0, 0.0, 0.0, 0.0, (double) depth, (double) q_value, p_value);
if(tsv) {
printsv(tsv_out, tsv, thread->template_name, aligned_assem, t_len, readCounts[template], read_score, expected, q_value, p_value, alignment_scores[template]);
=====================================
version.h
=====================================
@@ -17,4 +17,4 @@
* limitations under the License.
*/
-#define KMA_VERSION "1.4.7"
+#define KMA_VERSION "1.4.8"
View it on GitLab: https://salsa.debian.org/med-team/kma/-/commit/9bfc7814bd05f9c6585116e33c59dc8ef77348df
--
View it on GitLab: https://salsa.debian.org/med-team/kma/-/commit/9bfc7814bd05f9c6585116e33c59dc8ef77348df
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