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restructure MarkDup - adjust TagPileupWindow - remove CLI ext validation #134

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merged 6 commits into from
Oct 20, 2023
Merged

restructure MarkDup - adjust TagPileupWindow - remove CLI ext validation #134

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464faaa
restructure MarkDup to call picard form window
owlang Jun 1, 2023
4c92177
fix TagPileupWindow display spacing
owlang Jun 28, 2023
5aacbe5
change tag extend GUI default to 0
owlang Jun 29, 2023
f411d02
remove in/out extension restrictions on CLI tools
owlang Jun 29, 2023
149cfcd
Merge branch 'dev' into working-dev
owlang Jun 29, 2023
da81208
Merge branch 'dev' into working-dev
owlang Oct 12, 2023
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10 changes: 0 additions & 10 deletions src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtoBEDCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -106,10 +106,6 @@ private String validateInput() throws IOException {
r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
return(r);
}
//check input extensions
if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
}
//check BAI exists
File f = new File(bamFile+".bai");
if(!f.exists() || f.isDirectory()){
Expand All @@ -128,12 +124,6 @@ private String validateInput() throws IOException {
if(output!=null){ r += "(!)Cannot use -s flag with -o.\n"; }
//check output filename is valid
}else{
//check ext
try{
if(!"bed".equals(ExtensionFileFilter.getExtension(output))){
r += "(!)Use BED extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + ".bed\n";
}
} catch( NullPointerException e){ r += "(!)Output filename must have extension: use BED extension for output filename. Try: " + output + ".bed\n"; }
//check directory
if(output.getParent()==null){
// System.err.println("default to current directory");
Expand Down
10 changes: 0 additions & 10 deletions src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtoGFFCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -106,10 +106,6 @@ private String validateInput() throws IOException {
r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
return(r);
}
//check input extensions
if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
}
//check BAI exists
File f = new File(bamFile+".bai");
if(!f.exists() || f.isDirectory()){
Expand All @@ -128,12 +124,6 @@ private String validateInput() throws IOException {
if(output!=null){ r += "(!)Cannot use -s flag with -o.\n"; }
//check output filename is valid
}else{
//check ext
try{
if(!"gff".equals(ExtensionFileFilter.getExtension(output))){
r += "(!)Use GFF extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + ".gff\n";
}
} catch( NullPointerException e){ r += "(!)Output filename must have extension: use GFF extension for output filename. Try: " + output + ".gff\n"; }
//check directory
if(output.getParent()==null){
// System.err.println("default to current directory");
Expand Down
4 changes: 0 additions & 4 deletions src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtobedGraphCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -101,10 +101,6 @@ private String validateInput() throws IOException {
r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
return(r);
}
//check input extensions
if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
}
//check BAI exists
File f = new File(bamFile+".bai");
if(!f.exists() || f.isDirectory()){
Expand Down
10 changes: 0 additions & 10 deletions src/main/java/scriptmanager/cli/BAM_Format_Converter/BAMtoscIDXCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -103,10 +103,6 @@ private String validateInput() throws IOException {
r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
return(r);
}
//check input extensions
if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
}
//check BAI exists
File f = new File(bamFile+".bai");
if(!f.exists() || f.isDirectory()){
Expand All @@ -125,12 +121,6 @@ private String validateInput() throws IOException {
if(output!=null){ r += "(!)Cannot use -s flag with -o.\n"; }
//check output filename is valid
}else{
//check ext
try{
if(!"tab".equals(ExtensionFileFilter.getExtension(output))){
r += "(!)Use \".tab\" extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + ".tab\n";
}
} catch( NullPointerException e){ r += "(!)Output filename must have extension: use \".tab\" extension for output filename. Try: " + output + ".tab\n"; }
//check directory
if(output.getParent()==null){
// System.err.println("default to current directory");
Expand Down
18 changes: 0 additions & 18 deletions src/main/java/scriptmanager/cli/BAM_Manipulation/FilterforPIPseqCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -80,14 +80,6 @@ private String validateInput() throws IOException {
if (!r.equals("")) {
return (r);
}
// check input extensions
ExtensionFileFilter faFilter = new ExtensionFileFilter("fa");
if (!faFilter.accept(genomeFASTA)) {
r += "(!)Is this a FASTA file? Check extension: " + genomeFASTA.getName() + "\n";
}
if (!"bam".equals(ExtensionFileFilter.getExtension(bamFile))) {
r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
}
// check BAI exists
File f = new File(bamFile + ".bai");
if (!f.exists() || f.isDirectory()) {
Expand All @@ -105,16 +97,6 @@ private String validateInput() throws IOException {
output = new File(ExtensionFileFilter.stripExtension(bamFile) + "_PSfilter.bam");
// check output filename is valid
} else {
// check ext
try {
if (!"bam".equals(ExtensionFileFilter.getExtension(output))) {
r += "(!)Use BAM extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output)
+ ".bam\n";
}
} catch (NullPointerException e) {
r += "(!)Output filename must have extension: use BAM extension for output filename. Try: "
+ ExtensionFileFilter.stripExtension(output) + ".bam\n";
}
// check directory
if (output.getParent() == null) {
// System.err.println("default to current directory");
Expand Down
4 changes: 0 additions & 4 deletions src/main/java/scriptmanager/cli/BAM_Statistics/BAMGenomeCorrelationCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -135,9 +135,6 @@ private String validateInput() throws IOException {
//check input exists
if(!BAM.exists()|| BAM.isDirectory()){
r += "(!)BAM[" + x + "] file does not exist: " + BAM.getName() + "\n";
//check input extensions
}else if(!"bam".equals(ExtensionFileFilter.getExtension(BAM))){
r += "(!)Is this a BAM file? Check extension: " + BAM.getName() + "\n";
//check BAI exists
}else if(!BAI.exists() || BAI.isDirectory()){
r += "(!)BAI Index File does not exist for: " + BAM.getName() + "\n";
Expand All @@ -149,7 +146,6 @@ private String validateInput() throws IOException {
outputBasename = new File("correlation_matrix");
//check output filename is valid
}else{
//no check ext
//check directory
if(outputBasename.getParent()==null){
// System.err.println("default to current directory");
Expand Down
5 changes: 0 additions & 5 deletions src/main/java/scriptmanager/cli/BAM_Statistics/PEStatsCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -69,10 +69,6 @@ private String validateInput() throws IOException {
r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
return(r);
}
//check input extensions
if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
}
//check BAI exists
File f = new File(bamFile+".bai");
if(!f.exists() || f.isDirectory()){
Expand All @@ -84,7 +80,6 @@ private String validateInput() throws IOException {
outputBasename = new File(ExtensionFileFilter.stripExtension(bamFile));
//check output filename is valid
}else{
//no check ext
//check directory
if(outputBasename.getParent()==null){
// System.err.println("default to current directory");
Expand Down
5 changes: 0 additions & 5 deletions src/main/java/scriptmanager/cli/BAM_Statistics/SEStatsCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -61,10 +61,6 @@ private String validateInput() throws IOException {
r += "(!)BAM file does not exist: " + bamFile.getName() + "\n";
return(r);
}
//check input extensions
if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
r += "(!)Is this a BAM file? Check extension: " + bamFile.getName() + "\n";
}
//check BAI exists
File f = new File(bamFile+".bai");
if(!f.exists() || f.isDirectory()){
Expand All @@ -76,7 +72,6 @@ private String validateInput() throws IOException {
output = new File(ExtensionFileFilter.stripExtension(bamFile) + "_stats.txt");
//check output filename is valid
}else{
//no check ext
//check directory
if(output.getParent()==null){
// System.err.println("default to current directory");
Expand Down
20 changes: 1 addition & 19 deletions src/main/java/scriptmanager/cli/Figure_Generation/MergeHeatMapCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -38,8 +38,7 @@ public MergeHeatMapCLI(){}
@Parameters(index = "1", description = "Second(anti) PNG heatmap to merge, input2")
private File antiFile;

@Option(names = { "-o",
"--output" }, description = "specify output filename, please use PNG extension\n(default=\"<senseFile>_merged.png\" appended to the name in working directory of ScriptManager")
@Option(names = { "-o", "--output" }, description = "specify output filename, please use PNG extension\n(default=\"<senseFile>_merged.png\" appended to the name in working directory of ScriptManager")
private File output = null;

/**
Expand Down Expand Up @@ -76,29 +75,12 @@ private String validateInput() throws IOException {
if (!r.equals("")) {
return (r);
}
// check input extensions
if (!"png".equals(ExtensionFileFilter.getExtension(senseFile))) {
r += "(!)Is this a PNG file? Check extension: " + senseFile.getName() + "\n";
}
if (!"png".equals(ExtensionFileFilter.getExtension(antiFile))) {
r += "(!)Is this a PNG file? Check extension: " + antiFile.getName() + "\n";
}
// set default output filename
if (output == null) {
String NAME = ExtensionFileFilter.stripExtension(senseFile);
output = new File(NAME + "_merged.png");
// check output filename is valid
} else {
// check ext
try {
if (!"png".equals(ExtensionFileFilter.getExtension(output))) {
r += "(!)Use PNG extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output)
+ ".png\n";
}
} catch (NullPointerException e) {
r += "(!)Output filename must have extension: use PNG extension for output filename. Try: " + output
+ ".png\n";
}
// check directory
if (output.getParent() == null) {
// System.err.println("default to current directory");
Expand Down
14 changes: 0 additions & 14 deletions src/main/java/scriptmanager/cli/Figure_Generation/ThreeColorHeatMapCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -171,26 +171,12 @@ private String validateInput() throws IOException {
r += "(!)CDT file does not exist: " + CDT.getName() + "\n";
return (r);
}
// check input extensions
if (!"cdt".equals(ExtensionFileFilter.getExtension(CDT))) {
r += "(!)Is this a CDT file? Check extension: " + CDT.getName() + "\n";
}
// set default output filename
if (output == null) {
String NAME = ExtensionFileFilter.stripExtension(CDT);
output = new File(NAME + "_" + scaleType + ".png");
// check output filename is valid
} else {
// check ext
try {
if (!"png".equals(ExtensionFileFilter.getExtension(output))) {
r += "(!)Use PNG extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output)
+ ".png\n";
}
} catch (NullPointerException e) {
r += "(!)Output filename must have extension: use PNG extension for output filename. Try: " + output
+ ".png\n";
}
// check directory
if (output.getParent() == null) {
// System.err.println("default to current directory");
Expand Down
13 changes: 0 additions & 13 deletions src/main/java/scriptmanager/cli/Peak_Analysis/BEDPeakAligntoRefCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -71,24 +71,11 @@ private String validateInput() throws IOException {
r += "(!)BED-ref file does not exist: " + refBED.getName() + "\n";
}
if(!r.equals("")){ return(r); }
//check input extensions
if(!"bed".equals(ExtensionFileFilter.getExtension(peakBED))){
r += "(!)Is this a BED file? Check extension: " + peakBED.getName() + "\n";
}
if(!"bed".equals(ExtensionFileFilter.getExtension(refBED))){
r += "(!)Is this a BED file? Check extension: " + refBED.getName() + "\n";
}
//set default output filename
if(output==null){
output = new File(ExtensionFileFilter.stripExtension(peakBED) + "_" + ExtensionFileFilter.stripExtension(refBED) + "_Output.cdt");
//check output filename is valid
}else{
//check ext
try{
if(!"cdt".equals(ExtensionFileFilter.getExtension(output))){
r += "(!)Use CDT extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + ".cdt\n";
}
} catch( NullPointerException e){ r += "(!)Output filename must have extension: use CDT extension for output filename. Try: " + output + ".cdt\n"; }
//check directory
if(output.getParent()==null){
// System.err.println("default to current directory");
Expand Down
5 changes: 0 additions & 5 deletions src/main/java/scriptmanager/cli/Peak_Analysis/FilterBEDbyProximityCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -64,16 +64,11 @@ private String validateInput() throws IOException {
r += "(!)BED file does not exist: " + bedFile.getName() + "\n";
return(r);
}
//check input extensions
if(!"bed".equals(ExtensionFileFilter.getExtension(bedFile))){
r += "(!)Is this a BED file? Check extension: " + bedFile.getName() + "\n";
}
//set default output filename
if(outputBasename==null){
outputBasename = ExtensionFileFilter.stripExtension(bedFile) + "_" + Integer.toString(exclusion) + "bp";
//check output filename is valid
}else{
//no check ext
//check directory
File tmpOut = new File(outputBasename);
if(tmpOut.getParent()==null){
Expand Down
6 changes: 0 additions & 6 deletions src/main/java/scriptmanager/cli/Peak_Analysis/RandomCoordinateCLI.java
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Expand Up @@ -69,12 +69,6 @@ private String validateInput() throws IOException {
output = new File("random_coordinates_" + genomeName + "_" + numSites + "sites_" + window + "bp." + ext);
//check output filename is valid
}else{
//check ext
try{
if(!ext.equals(ExtensionFileFilter.getExtension(output))){
r += "(!)Use \"." + ext.toUpperCase() + "\" extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + "." + ext + "\n";
}
} catch( NullPointerException e){ r += "(!)Output filename must have extension: use \"." + ext.toUpperCase() + "\" extension for output filename. Try: " + output + "." + ext + "\n"; }
//check directory
if(output.getParent()==null){
// System.err.println("default to current directory");
Expand Down
6 changes: 0 additions & 6 deletions src/main/java/scriptmanager/cli/Peak_Analysis/TileGenomeCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -67,12 +67,6 @@ private String validateInput() throws IOException {
output = new File(genomeName + "_" + window + "bp." + ext);
//check output filename is valid
}else{
//check ext
try{
if(!ext.equals(ExtensionFileFilter.getExtension(output))){
r += "(!)Use \"." + ext.toUpperCase() + "\" extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output) + "." + ext + "\n";
}
} catch( NullPointerException e){ r += "(!)Output filename must have extension: use \"." + ext.toUpperCase() + "\" extension for output filename. Try: " + output + "." + ext + "\n"; }
//check directory
if(output.getParent()==null){
// System.err.println("default to current directory");
Expand Down
11 changes: 1 addition & 10 deletions src/main/java/scriptmanager/cli/Read_Analysis/ScalingFactorCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -93,19 +93,11 @@ private String validateInput() throws IOException {
if(!controlBAM.exists()){ r += "(!)BAM(control) file does not exist: " + controlBAM.getName() + "\n"; }
}
if(!r.equals("")){ return(r); }
//check input extensions & BAI exists
if(!"bam".equals(ExtensionFileFilter.getExtension(bamFile))){
r += "(!)Is this a BAM(input) file? Check extension: " + bamFile.getName() + "\n";
}
//check BAI exists
File f = new File(bamFile+".bai");
if(!f.exists() || f.isDirectory()){
r += "(!)BAI Index File does not exist for: " + bamFile.getName() + "\n";
}
if(blacklistFilter!=null){
if(!"bed".equals(ExtensionFileFilter.getExtension(blacklistFilter))){
r += "(!)Is this a BED file? Check extension: " + blacklistFilter.getName() + "\n";
}
}
if(controlBAM!=null){
if(!"bam".equals(ExtensionFileFilter.getExtension(controlBAM))){
r += "(!)Is this a BAM(control) file? Check extension: " + controlBAM.getName() + "\n";
Expand All @@ -121,7 +113,6 @@ private String validateInput() throws IOException {
//check output filename is valid
}else{
File tempOut = new File(outputBasename);
//no check ext
//check directory
if(tempOut.getParent()==null){
// System.err.println("default to current directory");
Expand Down
1 change: 0 additions & 1 deletion src/main/java/scriptmanager/cli/Read_Analysis/TagPileupCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -198,7 +198,6 @@ private String validateInput() throws IOException {
//check output COMPOSITE filename is valid
if(outputOptions.outputComposite!="composite_average.out"){
File output = new File(outputOptions.outputComposite);
//no check ext
//check directory
if(output.getParent()==null){
// System.err.println("default to current directory");
Expand Down
8 changes: 0 additions & 8 deletions src/main/java/scriptmanager/cli/Sequence_Analysis/DNAShapefromBEDCLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -131,14 +131,6 @@ private String validateInput() throws IOException {
if (!r.equals("")) {
return (r);
}
// check input extensions
ExtensionFileFilter faFilter = new ExtensionFileFilter("fa");
if (!faFilter.accept(genomeFASTA)) {
r += "(!)Is this a FASTA file? Check extension: " + genomeFASTA.getName() + "\n";
}
if (!"bed".equals(ExtensionFileFilter.getExtension(bedFile))) {
r += "(!)Is this a BED file? Check extension: " + bedFile.getName() + "\n";
}
// set default output filename
if (outputBasename == null) {
outputBasename = ExtensionFileFilter.stripExtension(bedFile);
Expand Down
6 changes: 0 additions & 6 deletions src/main/java/scriptmanager/cli/Sequence_Analysis/DNAShapefromFASTACLI.java
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Original file line number Diff line number Diff line change
Expand Up @@ -125,18 +125,12 @@ private String validateInput() throws IOException {
r += "(!)FASTA file does not exist: " + fastaFile.getName() + "\n";
return (r);
}
// check input extensions
ExtensionFileFilter faFilter = new ExtensionFileFilter("fa");
if (!faFilter.accept(fastaFile)) {
r += "(!)Is this a FASTA file? Check extension: " + fastaFile.getName() + "\n";
}
// set default output filename
if (outputBasename == null) {
outputBasename = ExtensionFileFilter.stripExtension(fastaFile);
// check output filename is valid
} else {
String outParent = new File(outputBasename).getParent();
// no extension check
// check directory
if (outParent == null) {
// System.err.println("default to current directory");
Expand Down
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