[med-svn] [Git][med-team/kma][upstream] New upstream version 1.3.3
Steffen Möller
gitlab at salsa.debian.org
Wed Sep 2 19:37:21 BST 2020
Steffen Möller pushed to branch upstream at Debian Med / kma
Commits:
a5deda4a by Steffen Moeller at 2020-09-02T20:16:01+02:00
New upstream version 1.3.3
- - - - -
5 changed files:
- align.c
- dist.c
- matrix.c
- nw.c
- version.h
Changes:
=====================================
align.c
=====================================
@@ -211,7 +211,6 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_
/* get best seed chain, returns best starting point */
start = chainSeedsPtr(points, q_len, t_len, kmersize, &aligned->mapQ);
score = points->score[start];
-
if(aligned->mapQ < mq || score < kmersize) {
Stat.score = 0;
Stat.len = 1;
@@ -342,7 +341,7 @@ AlnScore KMA(const HashMapCCI *template_index, const unsigned char *qseq, int q_
return Stat;
}
if((t_l > 0 || q_e - q_s > 0)) {
- band = 4 * abs(t_e - t_s - q_e + q_s) + bandwidth;
+ band = 4 * abs(t_l - q_e + q_s) + bandwidth;
if(q_e - q_s <= band || t_l <= band) {// || abs(t_e - t_s - q_e - q_s) >= 32) {
NWstat = NW(template_index->seq, qseq, 0, t_s, t_e, q_s, q_e, Frag_align, matrices);
} else {
=====================================
dist.c
=====================================
@@ -233,11 +233,11 @@ void kmerSimilarity_thread(HashMapKMA *DB, Matrix *Dist, int *N, int thread_num,
el = DB->v_index < UINT_MAX;
vs = DB->DB_size < USHRT_MAX;
D = Dist->mat;
- chunk = 1024;
+ chunk = 131072;
size = ((DB->size - 1) == DB->mask) ? DB->size : DB->n;
/* static init */
- lock(lock);
+ lockTime(lock, 10);
if(!thread_wait) {
thread_wait = thread_num;
next = 0;
@@ -249,7 +249,7 @@ void kmerSimilarity_thread(HashMapKMA *DB, Matrix *Dist, int *N, int thread_num,
/* get values */
while(n && chunk) {
/* get next chunk */
- lock(lock);
+ lockTime(lock, 10);
pos = next;
if(size < (next += chunk)) {
next = size;
@@ -337,8 +337,8 @@ void printIntLtdPhy(char *outfile, Matrix *Dist, int *N, FILE *name_file, Qseqs
/* init */
D = Dist->mat;
- chunk = 1048576;
- lock(lock);
+ chunk = 65536;
+ lockTime(lock, 10);
if(!row_bias) {
if(format & 4) {
row_bias += sprintf(outfile, "# %-35s\n", method);
@@ -361,9 +361,11 @@ void printIntLtdPhy(char *outfile, Matrix *Dist, int *N, FILE *name_file, Qseqs
unlock(lock);
while(next_i < Dist->n) {
- lock(lock);
+ lockTime(lock, 10);
/* check for new row */
- if(next_i <= next_j) {
+ if(Dist->n <= next_i) {
+ chunk = 0;
+ } else if(next_i <= next_j) {
i = ++next_i;
if(i) {
row_bias += (i - 1) * 11;
@@ -404,7 +406,7 @@ void printIntLtdPhy(char *outfile, Matrix *Dist, int *N, FILE *name_file, Qseqs
}
/* wait for matrix to finish */
- lock(lock);
+ lockTime(lock, 10);
if(--*thread_wait) {
unlock(lock);
wait_atomic(*thread_wait);
@@ -466,8 +468,8 @@ void printDoublePhy(char *outfile, Matrix *Dist, int *N, FILE *name_file, Qseqs
/* init */
D = Dist->mat;
- chunk = 1048576;
- lock(lock);
+ chunk = 65536;
+ lockTime(lock, 10);
if(!row_bias) {
if(format & 4) {
row_bias += sprintf(outfile, "# %-35s\n", method);
@@ -490,9 +492,11 @@ void printDoublePhy(char *outfile, Matrix *Dist, int *N, FILE *name_file, Qseqs
unlock(lock);
while(next_i < Dist->n) {
- lock(lock);
+ lockTime(lock, 10);
/* check for new row */
- if((ltd && next_i <= next_j) || (Dist->n <= next_j)) {
+ if(Dist->n <= next_i) {
+ chunk = 0;
+ } else if((ltd && next_i <= next_j) || (Dist->n <= next_j)) {
i = ++next_i;
if(i) {
row_bias += (ltd ? (i - 1) : Dist->n) * 11;
@@ -557,7 +561,7 @@ void printDoublePhy(char *outfile, Matrix *Dist, int *N, FILE *name_file, Qseqs
}
/* wait for matrix to finish */
- lock(lock);
+ lockTime(lock, 10);
if(--*thread_wait) {
unlock(lock);
wait_atomic(*thread_wait);
@@ -620,7 +624,7 @@ char * mfile(FILE *outfile, long unsigned size) {
ERROR();
}
rewind(outfile);
- outfileM = mmap(0, size, PROT_READ | PROT_WRITE, MAP_SHARED, fileno(outfile), 0);
+ outfileM = mmap(0, size, PROT_WRITE, MAP_SHARED, fileno(outfile), 0);
if(outfileM == MAP_FAILED) {
ERROR();
}
@@ -832,7 +836,9 @@ void runDist(char *templatefilename, char *outputfilename, int flag, int format,
free(threads);
threads = thread;
}
- munmap(outfileM - out_size, out_size);
+ outfileM -= out_size;
+ msync(outfileM, out_size, MS_SYNC);
+ munmap(outfileM, out_size);
fclose(outfile);
fclose(name_file);
free(N);
=====================================
matrix.c
=====================================
@@ -148,7 +148,11 @@ void Matrix_destroy(Matrix *src) {
void Matrix_mdestroy(Matrix *src) {
- munmap(*(src->mat), src->size * src->size * sizeof(int) / 2);
+ long unsigned size;
+
+ size = src->size * (src->size - 1) * sizeof(int) / 2;
+ msync(*(src->mat), size, MS_SYNC);
+ munmap(*(src->mat), size);
free(src->mat);
free(src);
}
=====================================
nw.c
=====================================
@@ -68,7 +68,7 @@ AlnScore NW(const long unsigned *template, const unsigned char *queryOrg, int k,
aligned->s[t_len] = 0;
memset(aligned->q, 5, t_len);
m = t_len;
- nuc_pos = t_e - 1;
+ nuc_pos = (t_e ? t_e : aligned->pos) - 1;
while(m--) {
aligned->t[m] = getNuc(template, nuc_pos);
if(--nuc_pos < 0) {
@@ -157,7 +157,6 @@ AlnScore NW(const long unsigned *template, const unsigned char *queryOrg, int k,
D_ptr[q_len] = (0 < k) ? 0 : (W1 + (t_len - 1 - m) * U);
Q_prev = (t_len + q_len) * (MM + U + W1);
-
t_nuc = getNuc(template, nuc_pos);
for(n = q_len - 1; n >= 0; --n) {
E_ptr[n] = 0;
@@ -344,7 +343,7 @@ AlnScore NW_band(const long unsigned *template, const unsigned char *queryOrg, i
aligned->s[t_len] = 0;
memset(aligned->q, 5, t_len);
m = t_len;
- nuc_pos = t_e - 1;
+ nuc_pos = (t_e ? t_e : aligned->pos) - 1;
while(m--) {
aligned->t[m] = getNuc(template, nuc_pos);
if(--nuc_pos < 0) {
=====================================
version.h
=====================================
@@ -17,4 +17,4 @@
* limitations under the License.
*/
-#define KMA_VERSION "1.3.2"
+#define KMA_VERSION "1.3.3"
View it on GitLab: https://salsa.debian.org/med-team/kma/-/commit/a5deda4a5ee6ea93c9d0732d1d955cf05160dada
--
View it on GitLab: https://salsa.debian.org/med-team/kma/-/commit/a5deda4a5ee6ea93c9d0732d1d955cf05160dada
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