increased buffer size globally and for fragment lines

shilpagarg · Jan 31, 2020 · eecb8b9 · eecb8b9
1 parent 639a34e
commit eecb8b9
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Showing 2 changed files with 5 additions and 6 deletions.
diff --git a/hapcut2-src/common.h b/hapcut2-src/common.h
@@ -7,7 +7,7 @@
 extern int QVoffset;
 extern int MINQ;
 
-#define MAXBUF 100000
+#define MAXBUF 1000000
 
 // given a=log10(x) and b=log10(y), returns log10(x+y)
 #define addlogs(a, b) (((a) > (b)) ? ((a) + log10(1.0 + pow(10.0, (b) - (a)))) : ((b) + log10(1.0 + pow(10.0, (a) - (b)))))
@@ -39,7 +39,7 @@ struct fragment {
     float htrans_prob; // probability of an h-trans interaction for this read
     int mate2_ix;     // snp index of second mate; -1 if this fragment has one mate
     int isize;        // approximate insert size
-    
+
     int PS; int PQ; char HP; // haplotype assignments for each fragment, HP= 0/1, PS = integer, PQ = probability that assignment of fragment is correct
 };
 
@@ -98,7 +98,7 @@ struct SNPfrags {
     float post_hap;
     int pruned_discrete_heuristic; // for error analysis mode
     float homozygous_prior; // prior probability of homozygousity. Based on GQ field of VCF.
-    float PGLL[5]; // phased genotype likelihoods, 00,01,10,11 and ./. (if variant is ignored) 
+    float PGLL[5]; // phased genotype likelihoods, 00,01,10,11 and ./. (if variant is ignored)
 };
 
 int fprintf_time(FILE *stream, const char *format, ...);

diff --git a/hapcut2-src/readinputfiles.c b/hapcut2-src/readinputfiles.c
@@ -19,9 +19,9 @@ int read_fragment_matrix(char* fragmentfile, struct fragment* Flist, int fragmen
     int i = 0, j = 0, k = 0, t = 0, t1 = 0, done = 0;
     int blocks = 0, type = 0, l = 0, biter = 0, offset = 0,dtype=0,isize = 0;
     char buffer[MAXBUF];
-    char blockseq[500000];
+    char blockseq[5000000];
     for (i=0;i<MAXBUF;i++) buffer[i] = 0;
-    for (i=0;i<500000;i++) blockseq[i] = 0;
+    for (i=0;i<5000000;i++) blockseq[i] = 0;
     char ch;
     int num_fields;
     int expected_num_fields;
@@ -473,4 +473,3 @@ int read_htrans_file(char* htrans_file, float* htrans_probs, int num_bins) {
 
     return 0;
 }
-