From a0f71f5eb6b3a6771d9d8e0bc1b5780c724d4cea Mon Sep 17 00:00:00 2001
From: arangrhie <arrhie@gmail.com>
Date: Wed, 14 Jul 2021 16:10:33 -0400
Subject: [PATCH] fix -completeness

---
 src/merfin/merfin-globals.C |  9 ---------
 src/merfin/merfin.C         | 10 ++++++++++
 2 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/src/merfin/merfin-globals.C b/src/merfin/merfin-globals.C
index acc18de..2f05f9a 100644
--- a/src/merfin/merfin-globals.C
+++ b/src/merfin/merfin-globals.C
@@ -114,11 +114,6 @@ merfinGlobal::getK(kmer     fmer,
 void
 merfinGlobal::load_Kmers(void) {
 
-  if (reportType == OP_COMPL) {
-    fprintf(stderr, "-- Not loading kmers; not necessary for -completeness mode.\n");
-    return;
-  }
-
   double            minMem, minMemTotal = 0;
   double            optMem, optMemTotal = 0;
   bool              useOpt = false;
@@ -175,10 +170,6 @@ merfinGlobal::load_Kmers(void) {
 void
 merfinGlobal::load_Sequence(void) {
 
-  if (reportType == OP_COMPL) {
-    return;
-  }
-
   if (seqDBname == nullptr) {
     seqDBname = new char[FILENAME_MAX+1];
     snprintf(seqDBname, FILENAME_MAX, "%s.meryl", basename(seqName));
diff --git a/src/merfin/merfin.C b/src/merfin/merfin.C
index aa7562f..3055631 100644
--- a/src/merfin/merfin.C
+++ b/src/merfin/merfin.C
@@ -160,6 +160,11 @@ main(int32 argc, char **argv) {
     if (G->peak == 0)  err.push_back("No haploid peak (-peak) supplied.\n");
   }
 
+  if (G->reportType == OP_COMPL) {
+    if (G->seqName == nullptr &&
+        G->seqDBname == nullptr) err.push_back("No sequence meryl database (-seqmers) nor sequence (-sequence) supplied.\n");
+  }
+
   if  (G->reportType == OP_NONE) {
     err.push_back("No report type (-filter, -polish, -hist, -dump, -completeness) supplied.\n");
   }
@@ -255,6 +260,11 @@ main(int32 argc, char **argv) {
     fprintf(stderr, "\n\n");
     fprintf(stderr, "  -completeness\n");
     fprintf(stderr, "   Compute kmer completeness using expected copy numbers for all kmers.\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "   Required: -seqmers (or -sequence), -readmers, -peak\n");
+    fprintf(stderr, "   Optional: -prob <file>  use probabilities to adjust multiplicity to copy number (recommended)\n");
+    fprintf(stderr, "\n");
+    fprintf(stderr, "   Output: total kmers in reads, number of kmers under the expected copy number, and completeness\n");
     fprintf(stderr, "\n\n");
     fprintf(stderr, "  Optional output from -debug in -filter and -polish:\n");
     fprintf(stderr, "   <output>.THREAD_ID.debug.gz : some useful info for debugging.\n");