[med-svn] [Git][med-team/kma][upstream] New upstream version 1.3.7
Nilesh Patra
gitlab at salsa.debian.org
Sat Nov 21 12:12:37 GMT 2020
Nilesh Patra pushed to branch upstream at Debian Med / kma
Commits:
c5c372bb by Nilesh Patra at 2020-11-21T17:39:21+05:30
New upstream version 1.3.7
- - - - -
5 changed files:
- hashmapcci.c
- hashmapcci.h
- runkma.c
- spltdb.c
- version.h
Changes:
=====================================
hashmapcci.c
=====================================
@@ -93,7 +93,7 @@ void hashMapCCI_destroy(HashMapCCI *dest) {
int hashMapCCI_get(const HashMapCCI *dest, long unsigned key, unsigned shifter) {
- unsigned index;
+ long unsigned index;
int pos, *chain;
/* get hash */
@@ -120,7 +120,7 @@ int hashMapCCI_get(const HashMapCCI *dest, long unsigned key, unsigned shifter)
int hashMapCCI_get_bound(const HashMapCCI *dest, long unsigned key, int min, int max, unsigned shifter) {
- unsigned index;
+ long unsigned index;
int pos, apos, *chain;
/* get hash */
@@ -148,7 +148,7 @@ int hashMapCCI_get_bound(const HashMapCCI *dest, long unsigned key, int min, int
int * hashMapCCI_getDubPos(const HashMapCCI *dest, long unsigned key, int value, unsigned shifter) {
- unsigned index;
+ long unsigned index;
int pos, *chain;
/* check input */
@@ -198,8 +198,7 @@ int defragChain(HashMapCCI *dest, int size, int shifter) {
/* defragmentize the chains to make space for new chain, return 0 on failure */
int newsize, cci_size, pos, newpos, index, fulldefrag;
int *newchain, *chain, *next;
- unsigned ipos;
- long unsigned kmer;
+ long unsigned ipos, kmer;
/* check if chain is available */
if(size <= dest->cci_avail) {
@@ -276,7 +275,8 @@ int defragChain(HashMapCCI *dest, int size, int shifter) {
int newChain(HashMapCCI *dest, int pos, int newpos, long unsigned kmer, int shifter) {
/* add new chain to hashmap */
- int index, *chain;
+ int *chain;
+ unsigned index;
if(4 <= dest->cci_avail) {
index = dest->cci_next;
@@ -307,7 +307,7 @@ int newChain(HashMapCCI *dest, int pos, int newpos, long unsigned kmer, int shif
int extendChain(HashMapCCI *dest, int chainpos, int newpos, long unsigned kmer, int shifter) {
int pos, dup, size, *chain, *newchain;
- unsigned index;
+ long unsigned index;
pos = chainpos;
chain = dest->chain + pos;
@@ -397,7 +397,7 @@ int extendChain(HashMapCCI *dest, int chainpos, int newpos, long unsigned kmer,
void hashMapCCI_add(HashMapCCI *dest, long unsigned key, int newpos, unsigned shifter) {
int pos, *index_ptr;
- unsigned index;
+ long unsigned index;
if(key == 0) {
/* likely undefined region */
@@ -424,7 +424,7 @@ void hashMapCCI_add_thread(HashMapCCI *dest, long unsigned key, int newpos, unsi
static volatile int indexLock[1] = {0}, cciLock[1] = {0};
int pos, *index_ptr;
- unsigned index;
+ long unsigned index;
if(key == 0) {
/* likely undefined region */
@@ -457,7 +457,7 @@ void hashMapCCI_add_thread(HashMapCCI *dest, long unsigned key, int newpos, unsi
HashMapCCI * hashMapCCI_load(HashMapCCI *src, int seq, int len, int kmersize) {
int i, end, shifter;
- long unsigned size;
+ long size;
/* init */
if(src == 0) {
@@ -469,7 +469,15 @@ HashMapCCI * hashMapCCI_load(HashMapCCI *src, int seq, int len, int kmersize) {
}
/* get seq */
- read(seq, src->seq, ((src->len >> 5) + 1) * sizeof(long unsigned));
+ size = ((src->len >> 5) + 1) * sizeof(long unsigned);
+ if(size != read(seq, src->seq, size)) {
+ if(0 < size) {
+ fprintf(stderr, "Corrupted *.seq.b\n");
+ exit(1);
+ } else {
+ ERROR();
+ }
+ }
/* add k-mers */
shifter = sizeof(long unsigned) * sizeof(long unsigned) - (src->kmerindex << 1);
@@ -486,6 +494,7 @@ HashMapCCI * hashMapCCI_load_thread(HashMapCCI *src, int seq, int len, int kmers
static volatile int lock[1] = {0}, next = 1, thread_wait = 0;
static long unsigned size;
int i, end, shifter, chunk;
+ long check;
/* init */
lock(lock);
@@ -496,7 +505,15 @@ HashMapCCI * hashMapCCI_load_thread(HashMapCCI *src, int seq, int len, int kmers
unlock(lock);
/* get seq */
- read(seq, src->seq, ((src->len >> 5) + 1) * sizeof(long unsigned));
+ check = ((src->len >> 5) + 1) * sizeof(long unsigned);
+ if(check != read(seq, src->seq, check)) {
+ if(check < 0) {
+ ERROR();
+ } else {
+ fprintf(stderr, "Corrupted *.seq.b\n");
+ exit(1);
+ }
+ }
} else {
unlock(lock);
}
=====================================
hashmapcci.h
=====================================
@@ -23,9 +23,9 @@
#ifndef HASHMAPCCI
typedef struct hashMapCCI HashMapCCI;
struct hashMapCCI {
- unsigned mask;
+ long unsigned mask;
unsigned len; // seqlen
- unsigned size; // size of index
+ long unsigned size; // size of index
unsigned kmerindex;
int *index; // k-mer posititions in seq / chain
int *chain; // k-mer collision positions
=====================================
runkma.c
=====================================
@@ -1396,6 +1396,9 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int
seqin_size = 4 * ftell(seq_in);
fseek(seq_in, 0, SEEK_SET);
seq_in_no = fileno(seq_in);
+ if(lseek(seq_in_no, 0, SEEK_SET) != 0) {
+ ERROR();
+ }
templatefilename[file_len] = 0;
/* allocate stuff */
@@ -2228,7 +2231,7 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int
thread->bcd = bcd;
thread->sam = sam;
thread->ef = extendedFeatures;
- thread->seq_in = fileno(seq_in);
+ thread->seq_in = seq_in_no;
thread->kmersize = kmersize;
thread->template = -2;
thread->file_count = fileCount;
@@ -2292,7 +2295,7 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int
thread->bcd = bcd;
thread->sam = sam;
thread->ef = extendedFeatures;
- thread->seq_in = fileno(seq_in);
+ thread->seq_in = seq_in_no;
thread->kmersize = kmersize;
thread->template = 0;
thread->file_count = fileCount;
@@ -2329,7 +2332,6 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int
if(verbose) {
fprintf(stderr, "# Template\tScore\tProgress\n");
}
-
for(template = 1; template < DB_size; ++template) {
if(w_scores[template] > 0) {
if(progress) {
=====================================
spltdb.c
=====================================
@@ -1541,6 +1541,9 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,
seqin_size = 4 * ftell(seq_in);
fseek(seq_in, 0, SEEK_SET);
seq_in_no = fileno(seq_in);
+ if(lseek(seq_in_no, 0, SEEK_SET) != 0) {
+ ERROR();
+ }
templatefilename[file_len] = 0;
strcat(templatefilename, ".name");
name_file = sfopen(templatefilename, "rb");
=====================================
version.h
=====================================
@@ -17,4 +17,4 @@
* limitations under the License.
*/
-#define KMA_VERSION "1.3.6"
+#define KMA_VERSION "1.3.7"
View it on GitLab: https://salsa.debian.org/med-team/kma/-/commit/c5c372bbfad911d7fe80e3aa1645d2e2572f6fdc
--
View it on GitLab: https://salsa.debian.org/med-team/kma/-/commit/c5c372bbfad911d7fe80e3aa1645d2e2572f6fdc
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