--with-missing-fields: fill AD={DP},0 for non-variant genotypes

src/spVCF.cc

@@ -541,7 +541,7 @@ class DecoderImpl : public TranscoderBase {
  bool with_missing_fields_;
  string format_;
  vector<string> format_split_;
- int iAD_ = -1, iPL_ = -1;
+ int iGT_ = -1, iDP_ = -1, iAD_ = -1, iPL_ = -1;
  // temp buffers used in add_missing_fields (to reduce allocations)
  OStringStream format_buffer_;
  string entry_copy_;
@@ -623,7 +623,11 @@ const char *DecoderImpl::ProcessLine(char *input_line) {
  split(format_copy, ':', back_inserter(format_split));
  for (int j = 0; j < format_split.size(); j++) {
  char *s = format_split[j];
- if (!strcmp(s, "AD")) {
+ if (!strcmp(s, "GT")) {
+ iGT_ = j;
+ } else if (!strcmp(s, "DP")) {
+ iDP_ = j;
+ } else if (!strcmp(s, "AD")) {
  iAD_ = j;
  } else if (!strcmp(s, "PL")) {
  iPL_ = j;
@@ -711,6 +715,7 @@ const char *DecoderImpl::ProcessLine(char *input_line) {
 // Most missing fields are just represented by . except for AD and PL, which we pad with . to the
 // correct vector length. (In principle we should do that for any Number={A,G,R} field, but this
 // suffices for our practical need for this feature.)
+// For non-variant genotypes we also fill AD={DP},0 if it'd otherwise be missing.
 void DecoderImpl::add_missing_fields(const char *entry, int n_alt, string &ans) {
  format_buffer_.Clear();
  entry_copy_ = entry;
@@ -725,7 +730,19 @@ void DecoderImpl::add_missing_fields(const char *entry, int n_alt, string &ans)
  if (i == iAD_ && (!present || !strcmp(field, "."))) {
  // FIXME: handle multiallelic. Meaning we need to run this on sparse entries too.
  // const int nAD = n_alt + 1;
- format_buffer_ << ".,.";
+ const char* gt = nullptr;
+ if (iGT_ >= 0 && iGT_ < entry_fields_.size()) {
+ gt = entry_fields_[iGT_];
+ }
+ const char* dp = nullptr;
+ if (iDP_ >= 0 && iDP_ < entry_fields_.size()) {
+ dp = entry_fields_[iDP_];
+ }
+ if (gt && dp && (strcmp(gt, "0/0") || strcmp(gt, "0|0") || strcmp(gt, "./.") || strcmp(gt, ".|."))) {
+ format_buffer_ << dp << ",0";
+ } else {
+ format_buffer_ << ".,.";
+ }
  } else if (i == iPL_ && (!present || !strcmp(field, "."))) {
  // const int nPL = (n_alt + 1) * (n_alt + 2) / 2;
  format_buffer_ << ".,.,.";