Refactor bio scripts and input setup

- Renamed `bio/inputs.sh` to `bio/deps.sh` and removed unnecessary code.
- Updated `bio/run.sh` to use the correct input file name.
- Removed unused code from `bio/input.sh`.
- Cleaned up `bio/verify.sh` and added comments.

Closes binpash#27

.github/workflows/tests.yml

@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        benchmark: [nlp, file-enc, unix50, log-analysis, max-temp, media-conv, sklearn, covid-mts, riker, oneliners, web-index]
+        benchmark: [nlp, file-enc, unix50, log-analysis, max-temp, media-conv, sklearn, covid-mts, riker, oneliners, web-index, bio]
 
     steps:
       - name: Checkout code

bio/inputs.sh → bio/deps.sh

@@ -1,22 +1,3 @@
-# red color
-RED='\033[0;31m'
-# reset the color
-NC='\033[0m'
-
-IN=${BIO4:-$PASH_TOP/benchmarks/bio}
-IN_NAME=${IN_N:-input_all.txt}
-if [[ $1 == "-c" ]]; then
-    rm -rf *.bam
-    rm -rf *.sam
-    rm -rf ../output
-    exit
-fi
-
-PW=${PASH_TOP}/benchmarks/bio/input
-echo $PW
-mkdir -p $PW
-mkdir -p ${PASH_TOP}/benchmarks/bio/output
-
 # install dependencies
 required_version="1.7"
 
@@ -62,17 +43,4 @@ else
         echo "Failed to install the correct version of Samtools."
         exit 1
     fi
-fi
-
-cat ${IN}/${IN_NAME} |while read s_line;
-	do
-
-    sample=$(echo $s_line |cut -d " " -f 2);
-    if [[ ! -f $sample ]]; then
-        pop=$(echo $s_line |cut -f 1 -d " ");
-        link=$(echo $s_line |cut -f 3 -d " ");
-        wget -O "$PW/$sample".bam  "$link"; ##this part can be adjusted maybe
-        # TODO: stop after one download for testing
-        exit 0
-    fi
-done;
+fi

bio/hashes/CHS_HG00614_1.hash

@@ -0,0 +1 @@
+527eb9f7611542301ec372574053e22f0437ee03a79d3e1bf6617b4b0bd18008

bio/hashes/CHS_HG00614_10.hash

@@ -0,0 +1 @@
+a7943043dcb526544ea0ec3dbe0bb2482e85d8997c603b28ec95d3e399bd7874

bio/hashes/CHS_HG00614_11.hash

@@ -0,0 +1 @@
+9fa8cc4dcaeb984e8c5acdf3f32e1859938f241c3949afbfb81c87cba4017215

bio/hashes/CHS_HG00614_17.hash

@@ -0,0 +1 @@
+8f155d4f0f892416c01ff79e9fbccefd255cbcac19e9df6c0df3768cb1588923

bio/hashes/CHS_HG00614_19.hash

@@ -0,0 +1 @@
+4322e91cde058dadffd216cb19cbb07696a828def8db10f23cddee49c12f1c04

bio/hashes/CHS_HG00614_2.hash

@@ -0,0 +1 @@
+bd1f91aca35c988469d8d9ebb7fb131349b3145a1b25950b18d3b7673a455f9a

bio/hashes/CHS_HG00614_4.hash

@@ -0,0 +1 @@
+b7e8d5f93d15a4f10556277c2841ee588782f485f09c33dcad2a4504e4433d65

bio/hashes/CHS_HG00614_7.hash

@@ -0,0 +1 @@
+d0c05e98f971cf18a7f0fa61a45ee4eb5c42b9c8ddf5b7f7d8b977e4232c463c

bio/hashes/CHS_HG00614_X.hash

@@ -0,0 +1 @@
+10f504af43506138056d60c3947de00bb7fc3b8b872c1eedc63d66a4d5586ead

bio/hashes/CHS_HG00614_Y.hash

@@ -0,0 +1 @@
+8cff7e9ec2c537298d6de6c0a1749d003c895549e32933dfd6eec94d376e0041

bio/hashes/HG00614_corrected.hash

@@ -0,0 +1 @@
+5b87bb001a505d9e0fe22b60d4c9303b90d4af001bbdc5e2038a0dcf7245dc76

bio/hashes/HG01942_corrected.hash

@@ -0,0 +1 @@
+e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855

bio/hashes/PEL_HG01942_1.hash

@@ -0,0 +1 @@
+fec413b3018fec127ff33d93219582195fd5286c9e6f01f1d58f365a62fbaecf

bio/hashes/PEL_HG01942_10.hash

@@ -0,0 +1 @@
+fec413b3018fec127ff33d93219582195fd5286c9e6f01f1d58f365a62fbaecf

bio/hashes/PEL_HG01942_11.hash

@@ -0,0 +1 @@
+fec413b3018fec127ff33d93219582195fd5286c9e6f01f1d58f365a62fbaecf

bio/hashes/PEL_HG01942_17.hash

@@ -0,0 +1 @@
+fec413b3018fec127ff33d93219582195fd5286c9e6f01f1d58f365a62fbaecf

bio/hashes/PEL_HG01942_19.hash

@@ -0,0 +1 @@
+fec413b3018fec127ff33d93219582195fd5286c9e6f01f1d58f365a62fbaecf

bio/hashes/PEL_HG01942_2.hash

@@ -0,0 +1 @@
+fec413b3018fec127ff33d93219582195fd5286c9e6f01f1d58f365a62fbaecf

bio/hashes/PEL_HG01942_4.hash

@@ -0,0 +1 @@
+fec413b3018fec127ff33d93219582195fd5286c9e6f01f1d58f365a62fbaecf

bio/hashes/PEL_HG01942_7.hash

@@ -0,0 +1 @@
+fec413b3018fec127ff33d93219582195fd5286c9e6f01f1d58f365a62fbaecf

bio/hashes/PEL_HG01942_X.hash

@@ -0,0 +1 @@
+fec413b3018fec127ff33d93219582195fd5286c9e6f01f1d58f365a62fbaecf

bio/hashes/PEL_HG01942_Y.hash

@@ -0,0 +1 @@
+fec413b3018fec127ff33d93219582195fd5286c9e6f01f1d58f365a62fbaecf

bio/input.sh

@@ -0,0 +1,31 @@
+# red color
+RED='\033[0;31m'
+# reset the color
+NC='\033[0m'
+
+IN=${BIO4:-$PASH_TOP/benchmarks/bio}
+IN_NAME=${IN_N:-input.txt}
+if [[ $1 == "-c" ]]; then
+    rm -rf *.bam
+    rm -rf *.sam
+    rm -rf ../output
+    exit
+fi
+
+PW=${PASH_TOP}/benchmarks/bio/input
+echo $PW
+mkdir -p $PW
+mkdir -p ${PASH_TOP}/benchmarks/bio/output
+
+cat ${IN}/${IN_NAME} |while read s_line;
+	do
+
+    sample=$(echo $s_line |cut -d " " -f 2);
+    if [[ ! -f $sample ]]; then
+        pop=$(echo $s_line |cut -f 1 -d " ");
+        link=$(echo $s_line |cut -f 3 -d " ");
+        wget -O "$PW/$sample".bam  "$link"; ##this part can be adjusted maybe
+        # stop after one download
+        exit 0
+    fi
+done;

bio/input.txt

@@ -1,2 +1 @@
 CHS HG00614 ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00614/cg_data/HG00614_lcl_SRR821831.mapped.COMPLETE_GENOMICS.CGworkflow2_2_evidenceOnly.CHS.high_coverage.20130401.bam 
-PEL HG01942 ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG01942/cg_data/HG01942_blood_SRR801093.mapped.COMPLETE_GENOMICS.CGworkflow2_2_evidenceOnly.PEL.high_coverage.20130401.bam 

bio/bio4.sh → bio/run.sh

@@ -1,7 +1,7 @@
 # create bam files with regions
 ################### 1KG SAMPLES
 IN=${INPUT:-$PASH_TOP/benchmarks/bio}
-IN_NAME=${IN_N:-input_all.txt}
+IN_NAME=${IN_N:-input.txt}
 OUT=${OUTPUT:-$PASH_TOP/benchmarks/bio/output}
 cat ${IN}/${IN_NAME}|while read s_line;
   do
@@ -22,7 +22,6 @@ cat ${IN}/${IN_NAME}|while read s_line;
     samtools view -b "${OUT}/$sample"_corrected.bam chr"$chr" > "${OUT}/$pop"_"$sample"_"$chr".bam ;
     echo 'Indexing Sample '$pop'_'${OUT}/$sample' ';
     samtools index -b "${OUT}/$pop"_"$sample"_"$chr".bam;
-    sleep 2
   done;
   #rm "${OUT}/$sample"_corrected.bam;
   #rm "${OUT}/$sample"_corrected.bam.bai;

bio/verify.sh

@@ -5,7 +5,9 @@
 
 cd "$(realpath $(dirname "$0"))"
 
-mkdir -p hashes
+hash_folder="hashes"
+
+mkdir -p $hash_folder
 
 if [[ "$@" == *"--generate"* ]]; then
     directory="output"
@@ -50,7 +52,7 @@ do
     for file in "$folder"/*.bam
     do
         current_file=$((current_file + 1))
-        echo "Processing file $current_file of $total_files..."
+        # echo "Processing file $current_file of $total_files..."
 
         # Extract the filename without the directory path and extension
         filename=$(basename "$file" .bam)
@@ -66,7 +68,8 @@ do
         # Compare the hash with the hash in the hashes directory
         diff "$hash_folder/$filename.hash" "$folder/$filename.hash"
 
-        # Print the filename and hash
-        echo "File: $folder/$filename | SHA-256 Hash: $(cat "$folder/$filename.hash")"
+        # # Print the filename and hash
+        # echo "File: $folder/$filename | SHA-256 Hash: $(cat "$folder/$filename.hash")"
     done
-done
+done
+exit 0