diff --git a/src/dssaligner.cpp b/src/dssaligner.cpp index 3a12157..64cddf3 100644 --- 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 index e898979..7850783 100644 --- 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 index e90cd69..c83838b 100644 --- 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 index 040516e..a4e5378 100644 --- 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 index 32bda52..fa7af26 100644 --- 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 index aaa556f..c735836 100644 --- 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 index 208036e..4ba91fa 100755 --- 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 index 4471ede..126b067 100755 --- 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