From 4c9ebe790be1d982c69b8ce45b73eeac08a9d6be Mon Sep 17 00:00:00 2001
From: Tobias Rausch <rauschtobi@gmail.com>
Date: Fri, 20 Sep 2024 15:39:39 +0200
Subject: [PATCH] fix lower case bug

---
 src/draw.h    | 16 ++++++++--------
 src/hilbert.h |  9 +++++----
 src/region.h  |  9 +++++----
 src/version.h |  2 +-
 4 files changed, 19 insertions(+), 17 deletions(-)

diff --git a/src/draw.h b/src/draw.h
index d80d5d3..b13bd1f 100644
--- a/src/draw.h
+++ b/src/draw.h
@@ -347,16 +347,16 @@ namespace wallysworld
     if (c.pxoffset >= WALLY_PX) {
       cv::Rect rect(x, y, w, h);
       cv::rectangle(img, rect, clr, -1);
-      if ((nuc == 'a') or (nuc == 'A')) {
+      if (nuc == 'A') {
 	cv::putText(img, text, cv::Point(x + w/2 - textSize.width/2, y+h/2+textSize.height/2), cv::FONT_HERSHEY_DUPLEX, font_scale, WALLY_A, font_thickness, cv::LINE_AA);
       }
-      else if ((nuc == 'c') or (nuc == 'C')) {
+      else if (nuc == 'C') {
       	cv::putText(img, text, cv::Point(x + w/2 - textSize.width/2, y+h/2+textSize.height/2), cv::FONT_HERSHEY_DUPLEX, font_scale, WALLY_C, font_thickness, cv::LINE_AA);
       }
-      else if ((nuc == 'g') or (nuc == 'G')) {
+      else if (nuc == 'G') {
 	cv::putText(img, text, cv::Point(x + w/2 - textSize.width/2, y+h/2+textSize.height/2), cv::FONT_HERSHEY_DUPLEX, font_scale, WALLY_G, font_thickness, cv::LINE_AA);
       }
-      else if ((nuc == 't') or (nuc == 'T')) {
+      else if (nuc == 'T') {
 	cv::putText(img, text, cv::Point(x + w/2 - textSize.width/2, y+h/2+textSize.height/2), cv::FONT_HERSHEY_DUPLEX, font_scale, WALLY_T, font_thickness, cv::LINE_AA);
       } else {  // n or N most likely
 	cv::putText(img, text, cv::Point(x + w/2 - textSize.width/2, y+h/2+textSize.height/2), cv::FONT_HERSHEY_DUPLEX, font_scale, WALLY_N, font_thickness, cv::LINE_AA);
@@ -365,16 +365,16 @@ namespace wallysworld
       int32_t pxw = w;
       if (pxw < 1) pxw = 1; // Make mismatches always visible
       cv::Rect rect(x, y, pxw, h);
-      if ((nuc == 'a') or (nuc == 'A')) {
+      if (nuc == 'A') {
 	cv::rectangle(img, rect, WALLY_A, -1);
       }
-      else if ((nuc == 'c') or (nuc == 'C')) {
+      else if (nuc == 'C') {
 	cv::rectangle(img, rect, WALLY_C, -1);
       }
-      else if ((nuc == 'g') or (nuc == 'G')) {
+      else if (nuc == 'G') {
 	cv::rectangle(img, rect, WALLY_G, -1);
       }
-      else if ((nuc == 't') or (nuc == 'T')) {
+      else if (nuc == 'T') {
 	cv::rectangle(img, rect, WALLY_T, -1);
       }
     }
diff --git a/src/hilbert.h b/src/hilbert.h
index 452c2d8..85bee5b 100644
--- a/src/hilbert.h
+++ b/src/hilbert.h
@@ -93,6 +93,7 @@ namespace wallysworld
 	if (seq != NULL) free(seq);
 	seq = faidx_fetch_seq(fai, hdr->target_name[rg[rgIdx].tid], 0, hdr->target_len[rg[rgIdx].tid], &seqlen);
 	oldchr = chrName;
+	boost::to_upper(seq);
       }
       
       // Parse BAM files
@@ -178,19 +179,19 @@ namespace wallysworld
 	uint32_t snpcov = cumsum;
 	cumsum += del[rpadj];
 	if (cumsum >= c.snvcov) {
-	  if ((seq[rp] == 'a') || (seq[rp] == 'A')) {
+	  if (seq[rp] == 'A') {
 	    if (((double) covA[rpadj] / (double) cumsum) < (1 - c.snvvaf)) {
 	      snp[rpadj] = true;
 	    }
-	  } else if ((seq[rp] == 'c') || (seq[rp] == 'C')) {
+	  } else if (seq[rp] == 'C') {
 	    if (((double) covC[rpadj] / (double) cumsum) < (1 - c.snvvaf)) {
 	      snp[rpadj] = true;
 	    }
-	  } else if ((seq[rp] == 'g') || (seq[rp] == 'G')) {
+	  } else if (seq[rp] == 'G') {
 	    if (((double) covG[rpadj] / (double) cumsum) < (1 - c.snvvaf)) {
 	      snp[rpadj] = true;
 	    }
-	  } else if ((seq[rp] == 't') || (seq[rp] == 'T')) {
+	  } else if (seq[rp] == 'T') {
 	    if (((double) covT[rpadj] / (double) cumsum) < (1 - c.snvvaf)) {
 	      snp[rpadj] = true;
 	    }
diff --git a/src/region.h b/src/region.h
index 4c3e86f..7e95b8c 100644
--- a/src/region.h
+++ b/src/region.h
@@ -159,6 +159,7 @@ namespace wallysworld
 	if (seq != NULL) free(seq);
 	seq = faidx_fetch_seq(fai, hdr->target_name[rg[rgIdx].tid], 0, hdr->target_len[rg[rgIdx].tid], &seqlen);
 	oldchr = chrName;
+	boost::to_upper(seq);
       }
 
       // Header
@@ -364,19 +365,19 @@ namespace wallysworld
 	  cumsum += covG[rpadj];
 	  cumsum += covT[rpadj];
 	  if (cumsum >= c.snvcov) {
-	    if ((seq[rp] == 'a') || (seq[rp] == 'A')) {
+	    if (seq[rp] == 'A') {
 	      if (((double) covA[rpadj] / (double) cumsum) < (1 - c.snvvaf)) {
 		snp[rpadj] = true;
 	      }
-	    } else if ((seq[rp] == 'c') || (seq[rp] == 'C')) {
+	    } else if (seq[rp] == 'C') {
 	      if (((double) covC[rpadj] / (double) cumsum) < (1 - c.snvvaf)) {
 		snp[rpadj] = true;
 	      }
-	    } else if ((seq[rp] == 'g') || (seq[rp] == 'G')) {
+	    } else if (seq[rp] == 'G') {
 	      if (((double) covG[rpadj] / (double) cumsum) < (1 - c.snvvaf)) {
 		snp[rpadj] = true;
 	      }
-	    } else if ((seq[rp] == 't') || (seq[rp] == 'T')) {
+	    } else if (seq[rp] == 'T') {
 	      if (((double) covT[rpadj] / (double) cumsum) < (1 - c.snvvaf)) {
 		snp[rpadj] = true;
 	      }
diff --git a/src/version.h b/src/version.h
index ca5fca1..78401f4 100644
--- a/src/version.h
+++ b/src/version.h
@@ -9,7 +9,7 @@ namespace wallysworld
 {
 
 
-  std::string wallyVersionNumber = "0.5.9";
+  std::string wallyVersionNumber = "0.6.1";
 
   inline 
     void printTitle(std::string const& title)