Merge branch 'master' of https://github.com/zhanxw/seqminer

zhanxw · Nov 27, 2023 · f050002 · f050002
2 parents 75c93ea + f5b374c
commit f050002
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/src/RangeList.h b/src/RangeList.h
@@ -346,7 +346,7 @@ class RangeList{
         positionPair(NULL){
       chromSize = rc.getChromVector().size();
       inChromRegionSize = getRegions(chromIndex)? getRegions(chromIndex)->size() : 0;
-      if (chromSize) {
+      if (chromSize && chromIndex < chromSize) {
         chrom = &(rc.getChromVector()[chromIndex]);
         positionPair = getRegions(chromIndex);
       }
@@ -358,7 +358,7 @@ class RangeList{
         this->inChromRangeIndex = 0;
         chromSize = this->rangeCollection->getChromVector().size();
         inChromRegionSize = getRegions(chromIndex)? getRegions(chromIndex)->size() : 0;
-        chrom = &(this->rangeCollection->getChromVector()[chromIndex]);
+        chrom = chromIndex < chromSize ? &(this->rangeCollection->getChromVector()[chromIndex]) : NULL;
         positionPair = getRegions(chromIndex);
       }
       return (*this);

diff --git a/src/SingleChromosomeBCFIndex.cpp b/src/SingleChromosomeBCFIndex.cpp
@@ -108,14 +108,15 @@ int SingleChromosomeBCFIndex::createIndex() {
   int64_t bgzf_offset_before_chrom = bgzf_tell(fp); // the offset to #CHROM
   s.resize(l_text - before_chrom_size);
   int64_t after_chrom_size = bgzf_read(fp, (void*) s.data(), l_text - before_chrom_size);
+  int32_t last_character = s[after_chrom_size - 1];
   // load sample names
   while (s.back() == '\n' || s.back() == '\0') {
     s.resize(s.size() - 1);
   }
   stringTokenize(s, "\t", &bcfHeader.sample_names);
   const int64_t num_sample = (int)bcfHeader.sample_names.size() - 9; // vcf header has 9 columns CHROM...FORMAT before actual sample names
   Rprintf("sample size = %ld\n", num_sample);
-  Rprintf("last character is s[after_chrom_size-1] = %d\n", s[after_chrom_size - 1]); // should be 0, the null terminator character
+  Rprintf("last character is s[after_chrom_size-1] = %d\n", last_character); // should be 0, the null terminator character
   // quality check
   if (bgzf_offset_after_header != bgzf_tell(fp)) {
     REprintf( "Messed up bgzf header\n");