[fix] Add VCF spanning deletion check

Issue: VCF v4.2 introduced the use of asterisk notation (*) in ALTs to represent spanning deletions. If there are alternative alleles at a site, the ‘*’ allele is reserved to indicate that an allele allele is missing due to an upstream deletion. This was not considered in angsd VCF reading and led to segfaults.
Fix: Add hasSpanningDeletion function to check if there is any spanning deletion and skip the sites with spanning deletion.
Fixes #557

Add development-related files to gitignore:
-vgcore files from valgrind
-commit_message.txt commit message template

.gitignore

@@ -48,3 +48,7 @@ misc/splitgl
 misc/supersim
 misc/thetaStat
 version.h
+
+# Development-related files
+vgcore*
+commit_message.txt

vcfReader.cpp

@@ -230,6 +230,26 @@ int isindel(const bcf_hdr_t *h, const bcf1_t *v){
 }
 
 
+/// @brief check if any allele is spanning deletion
+/// @param rec - bcf1_t record for one VCF line
+/// @return  1 : if any allele is deletion, 0 otherwise
+/// @details
+/// As of VCF 4.2, '*' is used to represent a spanning deletion if
+/// there are other alleles present at site. 
+int hasSpanningDeletion(const bcf1_t *rec){
+  if(rec->d.allele==NULL){
+    return 0;
+  }
+  for(int i=0;i<rec->n_allele;i++){
+    if(strncmp(rec->d.allele[i],"*",1)==0){
+        // fprintf(stderr,"\n[INFO]\t-> Skipping site at position %d. Reason: Found spanning deletion (%s).\n", (int)rec->pos+1, rec->d.allele[i]);
+      return 1;
+    }
+  }
+  return 0;
+}
+
+
 //type=0 -> PL
 //type=1 -> GL
 //type=2 -> GP
@@ -238,8 +258,9 @@ int dumpcounterverbose[2] = {0,0};
 int vcfReader::parseline(bcf1_t *rec,htsstuff *hs,funkyPars *r,int &balcon,int type){
   aio::doAssert(type>=0&&type<=2,1,AT,"");
   int n;
-  if(isindel(hs->hdr,rec)!=0)
+  if(isindel(hs->hdr,rec)!=0 || hasSpanningDeletion(rec)!=0){
     return 0;
+  }
 
   r->major[balcon] = refToChar[rec->d.allele[0][0]];
   r->minor[balcon] = refToChar[rec->d.allele[1][0]];
@@ -502,7 +523,7 @@ funkyPars *vcfReader::fetch(int chunkSize) {
 
     n++;
     //skip nonsnips
-    if(isindel(hs->hdr,rec)){
+    if(isindel(hs->hdr,rec)!=0 || hasSpanningDeletion(rec)){
       if(onlyprint>0){
 	fprintf(stderr,"\t Skipping due to non snp pos:%d (this message will be silenced after 10 sites)\n",(int)rec->pos+1);
 	onlyprint--;