--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fileIO/SummaryFile.java	Tue Mar 18 16:23:26 2025 -0400
@@ -0,0 +1,174 @@
+package fileIO;
+
+import java.io.File;
+
+import dna.Data;
+import shared.Parse;
+import shared.PreParser;
+
+/**
+ * Tests to see if a summary file matches a reference fasta file, based on date, size, and name
+ * @author Brian Bushnell
+ * @date Mar 11, 2013
+ *
+ */
+public class SummaryFile {
+	
+	public static void main(String[] args){
+		if(args.length==0){
+			System.out.println("Usage: SummaryFile <summary file> <reference fasta>");
+			System.exit(0);
+		}
+
+		{//Preparse block for help, config files, and outstream
+			PreParser pp=new PreParser(args, new Object() { }.getClass().getEnclosingClass(), false);
+			args=pp.args;
+			//outstream=pp.outstream;
+		}
+		
+		String summary=null, ref=null;
+		
+		for(int i=0; i<args.length; i++){
+
+			if(args[i].contains("=")){
+				final String arg=args[i];
+				final String[] split=arg.split("=");
+				String a=split[0].toLowerCase();
+				String b=split.length>1 ? split[1] : null;
+				
+				if(a.equals("summary")){
+					summary=b;
+				}else if(a.equals("ref") || a.equals("reference")){
+					ref=b;
+				}else{
+					throw new RuntimeException("Unknown parameter: "+args[i]);
+				}
+
+			}else{
+				if(args[i].endsWith("summary.txt")){
+					summary=args[i];
+				}else{
+					ref=args[i];
+				}
+			}
+		}
+		
+		if(summary==null && args.length>0){
+			summary=args[0];
+		}
+		
+		if(summary==null){
+			System.out.println("Usage: SummaryFile <summary file> <reference fasta>");
+			System.exit(0);
+		}
+		
+		if(ref==null){
+			
+		}
+	}
+	
+	public boolean compare(final String refName){
+		try {
+			File ref=new File(refName);
+			if(!ref.exists()){
+				if(refName.startsWith("stdin")){return false;}
+				else{
+					assert(false) : "No such file: "+refName;
+				}
+			}
+//			if(!refName.equals(source) && !Files.isSameFile(ref.toPath(), new File(source).toPath())){ //This is Java-7 specific.
+////				assert(false) : refName+", "+source+": "+(Files.isSameFile(ref.toPath(), new File(source).toPath()))+
+////						"\n"+ref.getCanonicalPath()+", "+new File(source).getCanonicalPath()+": "+(ref.getCanonicalPath().equals(new File(source).getCanonicalPath()));
+//				return false;
+//
+//			}
+			if(!refName.equals(source) && !ref.getCanonicalPath().equals(new File(source).getCanonicalPath())){
+//				assert(false) : refName+", "+source+": "+(Files.isSameFile(ref.toPath(), new File(source).toPath()))+
+//						"\n"+ref.getCanonicalPath()+", "+new File(source).getCanonicalPath()+": "+(ref.getCanonicalPath().equals(new File(source).getCanonicalPath()));
+				return false;
+				
+			}
+			if(bytes!=ref.length()){
+//				assert(false) : bytes+", "+ref.length();
+				return false;
+			}
+			if(modified!=ref.lastModified()){
+//				assert(false) : modified+", "+ref.lastModified();
+				return false;
+			}
+		} catch (Exception e) {
+			// TODO Auto-generated catch block
+			e.printStackTrace();
+			return false;
+		}
+		return true;
+	}
+	
+	public static boolean compare(final String summaryName, final String refName){
+		assert(refName!=null) : "Null reference file name.";
+		if(!new File(summaryName).exists()){
+//			assert(false);
+			return false;
+		}
+		SummaryFile sf=new SummaryFile(summaryName);
+		return sf.compare(refName);
+	}
+	
+	public static String getName(){
+		return getName(Data.GENOME_BUILD);
+	}
+	
+	public static String getName(int build){
+		return Data.ROOT_GENOME+build+"/summary.txt";
+	}
+	
+	public SummaryFile(String path){
+		summaryFname=path;
+		String s;
+		TextFile tf=new TextFile(summaryFname, false);
+		for(s=tf.nextLine(); s!=null; s=tf.nextLine()){
+			if(s.charAt(0)=='#'){
+				if(s.startsWith("#Version")){
+					String[] split=s.split("\t");
+					version=(split.length>1 ? Integer.parseInt(split[1]) : 0);
+				}
+			}else{
+				String[] split=s.split("\t");
+				String a=split[0];
+				String b=split[1];
+				if(a.equalsIgnoreCase("chroms")){chroms=(int)Long.parseLong(b);}
+				else if(a.equalsIgnoreCase("bases")){bases=Long.parseLong(b);}
+				else if(a.equalsIgnoreCase("version")){version=Integer.parseInt(b);}
+				else if(a.equalsIgnoreCase("defined")){definedBases=Long.parseLong(b);}
+				else if(a.equalsIgnoreCase("contigs")){contigs=Integer.parseInt(b);}
+				else if(a.equalsIgnoreCase("scaffolds")){scaffolds=Integer.parseInt(b);}
+				else if(a.equalsIgnoreCase("interpad")){interpad=Integer.parseInt(b);}
+				else if(a.equalsIgnoreCase("undefined")){undefinedBases=Long.parseLong(b);}
+				else if(a.equalsIgnoreCase("name")){name=b;}
+				else if(a.equalsIgnoreCase("source")){source=b;}
+				else if(a.equalsIgnoreCase("bytes")){bytes=Long.parseLong(b);}
+				else if(a.equalsIgnoreCase("last modified")){modified=Long.parseLong(b);}
+				else if(a.equalsIgnoreCase("scafprefixes")){scafprefixes=Parse.parseBoolean(b);}
+				else{throw new RuntimeException("In file "+tf.name+": Unknown term "+s);}
+			}
+		}
+		tf.close();
+	}
+
+	public final String summaryFname;
+
+	public int chroms;
+	public long contigs;
+	public long scaffolds;
+	public int interpad;
+	public long bases;
+	public long definedBases;
+	public long undefinedBases;
+	public String name;
+	public String source;
+	public int version;
+	public long bytes;
+	public long modified;
+	public boolean scafprefixes;
+	
+}