Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fileIO/CompressFiles.java @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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67:0e9998148a16 68:5028fdace37b
1 package fileIO;
2
3 import java.io.File;
4
5
6 public class CompressFiles {
7
8
9 public static void main(String[] args){
10 for(String s : args){
11 if(s.equalsIgnoreCase("zip")){
12 zip=true;
13 gzip=false;
14 }else if(s.equalsIgnoreCase("gzip") || s.equalsIgnoreCase("gz")){
15 zip=false;
16 gzip=true;
17 }else{
18 compressFiles(s);
19 }
20 }
21 }
22
23
24 public static void compressFiles(String path){
25 File f=new File(path);
26 compressFiles(f);
27 }
28
29 public static void compressFiles(File path){
30
31 if(path.isDirectory()){
32 File[] array=path.listFiles();
33 for(File f : array){compressFiles(f);}
34 }else{
35 compress(path);
36 }
37
38 }
39
40 public static void compress(File in){
41 assert(in.exists());
42 assert(in.isFile());
43 String abs=in.getAbsolutePath();
44 // System.out.println("Considering "+abs);
45 if(abs.endsWith(".gz") || abs.endsWith(".zip") || abs.endsWith(".bz2")){return;}
46
47 // if(!abs.contains("custom_summary_") || !abs.endsWith("Gene_build36.txt")){return;} //TODO ***TEMPORARY***
48 System.err.println(abs);
49 // if(!abs.endsWith(".gvla")){return;} //TODO ***TEMPORARY***
50 // if(!abs.endsWith(".gvla") ||
51 // !(abs.contains("seqGene") || abs.contains("refGene") || abs.contains("unionGene"))){return;} //TODO ***TEMPORARY***
52 if(abs.toLowerCase().contains("familytree")){return;} //TODO ***TEMPORARY***
53
54 if(PRINT_7Z_BATCH){
55 //-mx=4 is fast; -mx=5 or 6 is slow; 7+ is very slow.
56 // System.out.println("C:"+Data.SLASH+"\"Program Files\""+Data.SLASH+"7-Zip"+Data.SLASH+"7z a -mx=4 "+abs+".zip "+abs);
57 System.out.println("C:\\\"Program Files\"\\7-Zip\\7z a -mx=4 "+abs+".gz "+abs);
58 }else{
59 System.out.println("Compressing "+abs+" to "+(zip ? "zip" : "gz"));
60 ReadWrite.copyFile(abs, abs+(zip ? ".zip" : ".gz"));
61 }
62
63 }
64
65
66 public static boolean zip=true;
67 public static boolean gzip=!zip;
68
69 public static boolean PRINT_7Z_BATCH=true;
70
71 }