Prep for updating release 2.0 with AQ

rcedgar · Oct 29, 2024 · e86cff4 · e86cff4
1 parent 5e90cc4
commit e86cff4
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Showing 8 changed files with 10 additions and 8 deletions.
diff --git a/src/dssaligner.cpp b/src/dssaligner.cpp
@@ -144,7 +144,7 @@ DSSAligner::DSSAligner()
 		}
 	else
 		{
-		m_UFs.push_back(UF_qual);
+		m_UFs.push_back(UF_aq);
 		m_UFs.push_back(UF_query);
 		m_UFs.push_back(UF_target);
 		m_UFs.push_back(UF_evalue);

diff --git a/src/dssaligner.h b/src/dssaligner.h
@@ -173,7 +173,7 @@ class DSSAligner
 	float GetNewTestStatistic(bool Top) const { return Top ? m_NewTestStatisticA : m_NewTestStatisticB; }
 	//float GetAvgTestStatistic() const { return (m_TestStatisticA + m_TestStatisticB)/2; }
 	float GetEvalue(bool Top) const { return Top ? m_EvalueA : m_EvalueB; }
-	float GetQuality(bool Top) const { return Top ? m_QualityA : m_QualityB; }
+	float GetAQ(bool Top) const { return Top ? m_QualityA : m_QualityB; }
 
 	void GetRow(bool Up, bool Top, bool Global, string &Row) const;
 

diff --git a/src/usage.h b/src/usage.h
@@ -36,13 +36,14 @@ const char *usage_txt[] =
 "                 #   tl      Target length\n"
 "                 #   pctid   Percent identity of alignment\n"
 "                 #   cigar   CIGAR string\n"
+"                 #   aq      AQ (aln. qual., 0 .. 1, >0.5 suggests homology)\n"
 "                 #   evalue  You can guess this one\n"
 "                 #   qrow    Aligned query sequence with gaps (local)\n"
 "                 #   trow    Aligned target sequence with gaps (local)\n"
 "                 #   qrowg   Aligned query sequence with gaps (global)\n"
 "                 #   trowg   Aligned target sequence with gaps (global)\n"
 "                 #   std     query+target+qlo+qhi+ql+tlo+thi+tl+pctid+evalue\n"
-"                 # default evalue+query+target\n"
+"                 # default aq+query+target+evalue\n"
 "\n"
 "Search and alignment options\n"
 "  -fast, -sensitive or -verysensitive     # Required\n"

diff --git a/src/userfieldnames.h b/src/userfieldnames.h
@@ -23,6 +23,6 @@ x(dpscore)
 x(lddt)
 x(ids)
 x(gaps)
-x(qual)
+x(aq)
 
 #undef x
diff --git a/src/userfields.cpp b/src/userfields.cpp
@@ -115,9 +115,9 @@ void DSSAligner::WriteUserField(FILE *f, USERFIELD UF, bool Up) const
 		break;
 		}
 
-	case UF_qual:
+	case UF_aq:
 		{
-		fprintf(f, "%.4f", GetQuality(Up));
+		fprintf(f, "%.4f", GetAQ(Up));
 		break;
 		}
 

diff --git a/test_results/success_list.txt b/test_results/success_list.txt
@@ -8,3 +8,4 @@ reseekv2.0.i86linux64[32d9850]	2024-10-26/09:57:22
 reseekv2.0.i86linux64[25a1340]	2024-10-28/07:32:40
 reseekv2.0.i86linux64[854fa22]	2024-10-28/08:30:48
 reseekv2.0.i86linux64[e2fa7e1]	2024-10-28/17:34:37
+reseekv2.0.i86linux64[5e90cc4]	2024-10-29/15:43:38
diff --git a/test_scripts/check_columns.py b/test_scripts/check_columns.py
@@ -70,7 +70,7 @@ def check_default(fn):
         try:
             Q = float(flds[0])
         except:
-            print("ERROR %s qual %s not float" % (fn, flds[0]))
+            print("ERROR %s aq %s not float" % (fn, flds[0]))
             errors += 1
             return
         try:

diff --git a/test_scripts/columns.bash b/test_scripts/columns.bash
@@ -11,7 +11,7 @@ $reseek \
 $reseek \
 	-search dir.bca \
 	-fast \
-	-columns qual+query+target+evalue \
+	-columns aq+query+target+evalue \
 	-output columns_same_as_default.tsv \
 	-log columns_same_as_default.log
-Original file line number
+Diff line change
@@ Expand Up / @@ -23,6 +23,6 @@ x(dpscore) @@
     x(lddt)
     x(ids)
     x(gaps)
-    x(qual)
+    x(aq)
     #undef x