From df8400617956bd0c62964dfddcba5be86df5df6a Mon Sep 17 00:00:00 2001
From: Guoyi Zhang <kuoi@bioarchlinux.org>
Date: Fri, 5 Jul 2024 11:53:06 +1000
Subject: [PATCH] add: more comments

---
 RGBEPP.sh       | 10 ++++++++++
 sortdiamond.cpp |  3 +++
 2 files changed, 13 insertions(+)

diff --git a/RGBEPP.sh b/RGBEPP.sh
index 4b2f408..6c5e87e 100644
--- a/RGBEPP.sh
+++ b/RGBEPP.sh
@@ -303,6 +303,7 @@ if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "pre" ]; then
 	check_var "ARG_L"
 	check_path "PathSortdiamond"
 
+	# extract fasta file from diamond balst style output
 	for (( i=0; i<$length_fn; i++ )); do	
 		$PathSortdiamond $DirMap/${full_names[$i]}.m8 $DirPre/${full_names[$i]}.fasta
 	done
@@ -316,9 +317,12 @@ if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "split" ]; then
 	check_var "ARG_L"
 	check_path "PathSplitfasta"
 
+	# split fasta into different folders based on sequence names
 	for (( i=0; i<$length_fn; i++ )); do
 		$PathSplitfsata ${full_names[$i]}.fasta
 	done
+
+	# mv to destdir
 	find . -mindepth 1 -maxdepth 1 -type d -exec mv {} ../$DirSplit \;
 	cd -
 fi
@@ -330,13 +334,18 @@ if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "merge" ]; then
 
 	mkdir -p $DirMerge
 	cd $DirSplit
+
+	# merge different taxa sequences in same gene to one fasta 
 	for (( i=0; i<$length_gn; i++ )) 
 	do
 		cd ${genes[$i]}
 		cat * > ../${genes[$i]}.fasta
 		cd ..
 	done
+
+	# mv to destdir
 	mv *.fasta ../$DirMerge
+
 	cd -
 	
 fi
@@ -354,6 +363,7 @@ if [ "$ARG_F" = "all" ] || [ "$ARG_F" = "align" ]; then
 	mkdir -p $DirAlign/AA && mkdir -p $DirAlign/NT
 	cd $DirMerge
 
+	# align the sequence based on codon
 	parallel -j $ARG_T java -jar $PathMacse -prog alignSequences -seq {}.fasta -out_AA ../$DirAlign/AA/{}.fasta -out_NT ../$DirAlign/NT/{}.fasta ::: "${genes[@]}"
 
 	cd -
diff --git a/sortdiamond.cpp b/sortdiamond.cpp
index 3141dac..75cf8b9 100644
--- a/sortdiamond.cpp
+++ b/sortdiamond.cpp
@@ -80,7 +80,9 @@ void readInputFile(const string &filename,
 		while (iss >> fields[i] && i < 20) {
 			i++;
 		}
+		// subject seq id
 		string key = fields[1];
+		// bit score
 		double value = stod(fields[11]);
 		// Check if the key already exists in the map
 		if (max_map.find(key) != max_map.end()) {
@@ -106,6 +108,7 @@ void processMap(const map<string, pair<double, string>> &max_map,
 		while (iss >> fields[i] && i < 20) {
 			i++;
 		}
+		// check if qstart is larger than qend
 		if (stoi(fields[6]) > stoi(fields[7])) {
 			fields[17] = revcomp(fields[17]);
 		}