From 1a1db870b9220216b5a13296e1d036d8baf05e34 Mon Sep 17 00:00:00 2001
From: "Brian P. Walenz" <thebri@gmail.com>
Date: Wed, 3 Mar 2021 19:43:42 -0500
Subject: [PATCH] Save results in memory, write them to the actual output file
 instead of temporary files.

---
 src/merfin/merfin-globals.H  | 11 ++++++++---
 src/merfin/merfin-variants.C | 20 +++++++++-----------
 2 files changed, 17 insertions(+), 14 deletions(-)

diff --git a/src/merfin/merfin-globals.H b/src/merfin/merfin-globals.H
index d2138d2..7dca9e1 100644
--- a/src/merfin/merfin-globals.H
+++ b/src/merfin/merfin-globals.H
@@ -82,6 +82,7 @@ public:
 
   //  Variant results.
 
+  string     result;
   //uint64     vmersLen    = 0;
   //uint64     vmersMax    = 0;
   //char      *vmers       = nullptr;
@@ -102,7 +103,6 @@ public:
   }
   ~merfinThrData() {
     delete oDebug;
-    delete oVcf;
   }
 
   //  Our ident.
@@ -113,8 +113,6 @@ public:
 
   compressedFileWriter   *oDebug   = nullptr;
   uint64                  varMerId = 0;
-
-  compressedFileWriter   *oVcf     = nullptr;
 };
 
 
@@ -132,8 +130,15 @@ public:
 class merfinGlobal {
 public:
   ~merfinGlobal() {
+    delete dumpOutFile;
+    delete oVCF;
+
+    delete [] histUndr;
+    delete [] histOver;
+
     delete seqFile;
     delete inVcf;
+
     delete asmLookup;
     delete readLookup;
   }
diff --git a/src/merfin/merfin-variants.C b/src/merfin/merfin-variants.C
index c248e9e..f7d2b6d 100644
--- a/src/merfin/merfin-variants.C
+++ b/src/merfin/merfin-variants.C
@@ -149,14 +149,8 @@ processVariants(void *G, void *T, void *S) {
   if (t->oDebug == nullptr) {
     char  name[FILENAME_MAX+1];
 
-    snprintf(name, FILENAME_MAX, "%s.%02d.debug", g->outName, t->threadID);
+    snprintf(name, FILENAME_MAX, "%s.%02d.debug.gz", g->outName, t->threadID);
     t->oDebug = new compressedFileWriter(name);
-
-    snprintf(name, FILENAME_MAX, "%s.%02d.vcf", g->outName, t->threadID);
-    t->oVcf = new compressedFileWriter(name);
-
-    for (string header : g->inVcf->getHeaders())
-      fprintf(t->oVcf->file(), "%s\n", header.c_str());
   }
 
   //  Get chromosome specific posGTs, and iterate over.
@@ -286,7 +280,8 @@ processVariants(void *G, void *T, void *S) {
 
     // Experimental: output vcf according to k*
     if (g->bykstar) {
-      fprintf(t->oVcf->file(), "%s", seqMer->bestVariant().c_str());
+      //fprintf(t->oVcf->file(), "%s", seqMer->bestVariant().c_str());
+      s->result += seqMer->bestVariant();
     }
 
     // Filter vcf and print as it was in the original vcf, conservatively
@@ -294,7 +289,8 @@ processVariants(void *G, void *T, void *S) {
       vector<vcfRecord*> records = seqMer->bestVariantOriginalVCF();
 
       for (uint64 i = 0; i < records.size(); i++)
-        records[i]->save(t->oVcf);
+        //records[i]->save(t->oVcf);
+        s->result += records[i]->save();
     }
 
     //  Cleanup.
@@ -329,9 +325,11 @@ outputVariants(void *G, void *S) {
       fprintf(g->oVCF->file(), "%s\n", header.c_str());
   }
 
-  //
-
+  //  Dump the output string to the output file.  Flush it just
+  //  so we can get a reliable record of where we are.
 
+  fputs(s->result.c_str(), g->oVCF->file());
+  fflush(g->oVCF->file());
 
   //  Bye.