Enable compressed fastq reading and writing

.gitlab-ci.yml

@@ -19,5 +19,5 @@ build_conda:
   script:
     - anaconda login --username "$DOCKER_USER" --password "$DOCKER_PASS"
     - conda build conda_inst
-  only:
+  except:
     - master
\ No newline at end of file

conda_inst/meta.yaml

@@ -9,8 +9,10 @@ channels:
     - defaults
 
 source:
-  url: ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/AlienTrimmer_0.4.0.tar.gz
-  md5: 8ed76aafea9fef48f49d74b59025212d
+  - git_url: https://gitlab.pasteur.fr/aghozlan/shaman.git
+    git_rev: {{ environ.get('GIT_DESCRIBE_TAG', '') }}
+  #url: ftp://ftp.pasteur.fr/pub/gensoft/projects/AlienTrimmer/AlienTrimmer_0.4.0.tar.gz
+  #md5: 8ed76aafea9fef48f49d74b59025212d
 
 requirements:
     host:

src/AlienTrimmer.java

@@ -70,6 +70,8 @@
 
 import java.io.*;
 import java.util.*;
+import java.util.zip.GZIPInputStream;
+import java.util.zip.GZIPOutputStream;
 
 public class AlienTrimmer {
 
@@ -336,6 +338,14 @@ public class AlienTrimmer {
 		System.exit(0);
 	    }
 	}
+  String finfilename = finfile.toString();
+  String rinfilename = rinfile.toString();
+  String foutfilename = foutfile.toString();
+  String routfilename = routfile.toString();
+  String finext = finfilename.substring(finfilename.lastIndexOf(".") + 1, finfilename.length());
+  String rinext = rinfilename.substring(rinfilename.lastIndexOf(".") + 1, rinfilename.length());
+  String foutext = foutfilename.substring(foutfilename.lastIndexOf(".") + 1, foutfilename.length());
+  String routext = routfilename.substring(routfilename.lastIndexOf(".") + 1, routfilename.length());
 	//### testing default variables ##############################################################################
 	if ( finfile.toString().equals("no.file") ) { System.out.println("  no input file"); System.exit(1); }
 	if ( foutfile.toString().equals("no.file") ) foutfile = new File(finfile + ".at.fq");
@@ -346,14 +356,13 @@ public class AlienTrimmer {
 	}
 	if ( mismatch < B0 ) { mismatch = k; ++mismatch; mismatch /= B2; }
 	//### detecting Phred encoding ##############################################################################
-  if ( finfile.toString().equals(".gz") ){ 
-  try (GZIPInputStream in = new GZIPInputStream(new FileInputStream(input))){
-  }
-	phred = 0; fin = new BufferedReader(new FileReader(finfile)); 
+	phred = 0; //fin = new BufferedReader(new FileReader(finfile));
+  if(finext.equals("gz") || finext.equals("gzip")) fin = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(finfile))));
+  else fin = new BufferedReader(new FileReader(finfile)); 
 	cpt = B0; 
 	while ( phred == 0 ) {		
 	    //## reading fastq ##
-	    try { line = fin.readLine().trim(); } catch ( NullPointerException e ) { fin.close(); break; }
+      try { line = fin.readLine().trim(); } catch ( NullPointerException e ) { fin.close(); break; }
 	    switch ( ++cpt ) { case B1: case B2: case B3: continue; case B4: fqsc = line; cpt = B0; break; }
 	    i = (short) fqsc.length(); while ( --i >= 0 ) { if ( fqsc.charAt(i) <= '9' ) { phred = 33; break; } if ( fqsc.charAt(i) >= 'L' ) { phred = 64; break; } }
 	}
@@ -509,22 +518,24 @@ public class AlienTrimmer {
 	    //####################
 	    //## trimming reads ##
 	    //####################
-	    fin = new BufferedReader(new FileReader(finfile)); fout = new BufferedWriter(new FileWriter(foutfile));
+      if(finext.equals("gz") || finext.equals("gzip")) fin = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(finfile))));
+      else fin = new BufferedReader(new FileReader(finfile));
+      if(foutext.equals("gz") || foutext.equals("gzip")) fout = new BufferedWriter(new OutputStreamWriter(new GZIPOutputStream(new FileOutputStream(foutfile))));
+      else fout = new BufferedWriter(new FileWriter(foutfile));
 	    pcpt = 0; ftcpt = 0; frcpt = 0;
 	    cpt = B0; score = new byte[51];
-	    while ( true ) {		
-		//## reading fastq ##
-		try { line = fin.readLine().trim(); } catch ( NullPointerException e ) { fin.close(); break; }
-		switch ( ++cpt ) { case B1: fid1 = line; continue; case B2: fseq = line; continue; case B3: fid2 = line; continue; case B4: fqsc = line; cpt = B0; break; }
-		
-		//## displaying info ##
+      while ( true ) {
+    //## reading fastq ##
+    try { line = fin.readLine().trim(); } catch ( NullPointerException e ) { fin.close(); break; }
+    switch ( ++cpt ) { case B1: fid1 = line; continue; case B2: fseq = line; continue; case B3: fid2 = line; continue; case B4: fqsc = line; cpt = B0; break; }
+    
+    //## displaying info ##
 		if ( ++pcpt % 1000000 == 0 ) 
 		    System.out.println("[" + String.format(Locale.US, "%02d", new Long((cur=(System.currentTimeMillis()-t)/1000)/60))
 				       + ":" + (line="0"+(cur%60)).substring(line.length()-2) + "]" 
 				       + String.format(Locale.US, "%,12d", new Integer(pcpt)) + " reads processed:" 
 				       + String.format(Locale.US, "%,12d", new Integer(ftcpt)) + " trimmed" 
 				       + String.format(Locale.US, "%,12d", new Integer(frcpt)) + " removed");
-		
 		//## matching k-mers... ##
 		if ( (lgt=(short)fseq.length()) < minLgt ) { ++frcpt; continue; } // too small read
 		if ( lgt >= score.length ) { score = new byte[++lgt]; --lgt; } else Arrays.fill(score, B0);
@@ -552,12 +563,12 @@ public class AlienTrimmer {
 			case 'G': case 'g': iptn |= B2; lptn |= B4; nptn |= B4;  break; 
 			case 'T': case 't': iptn |= B3; lptn |= B8; nptn |= B8;  break; 
 			default:  n = k;                            nptn |= B15; 
-			} 
+			}
 			switch ( (((--n) < B0) ? B0 : B1) ) {
 			case B0:
 			    if ( bsfkmer.get((iptn &= imsk)) ) { 
-				b = (score[i]=(++b)); score[i] += bq; --score[++j]; 
-				scount += B2; start0 = ( start0 < B0 ) ? ((short)(B2*i)) : start0; 
+				b = (score[i]=(++b)); score[i] += bq; --score[++j];
+				scount += B2; start0 = ( start0 < B0 ) ? ((short)(B2*i)) : start0;
 				//start = ( /*(i-start <= k2) &&*/ (j >= start0) && (scount+k2 >= j) ) ? j : ++start; --start;
 				start = ( (j >= start0) && (scount+k2 >= j) ) 
 				    ? (( start < B0 ) ? j : (( i-start <= mismatch ) ? j : ++start)) 
@@ -580,7 +591,7 @@ public class AlienTrimmer {
 			    }
 			    break;
 			}
-			b = (score[i]=((b < B0) ? B0 : b)); ++j; 
+			b = (score[i]=((b < B0) ? B0 : b)); ++j;
 			if ( (score[i] += bq) == B0 ) continue;
 			scount += B2; start0 = ( start0 < B0 ) ? ((short)(B2*i)) : start0;
 			start = ( (start < i) && ((x=i)-start <= mismatch) && ((++x) >= start0) && (scount > x) ) ? i : start; end = i; 
@@ -607,6 +618,7 @@ public class AlienTrimmer {
 			}
 			b = (score[i]=((b < B0) ? B0 : b)); ++j; 
 			if ( (score[i] += bq) == B0 ) continue;
+      //Very strange
 			scount += B2; start0 = ( start0 < B0 ) ? ((short)(B2*i)) : start0;
 			start = ( (start < i) && ((x=i)-start <= mismatch) && ((++x) >= start0) && (scount > x) ) ? i : start; end = i; 
 		    }
@@ -681,14 +693,15 @@ public class AlienTrimmer {
 		o = B_1; while ( ++o < lgt ) System.out.print( (( (b=score[o]) == B0 ) ? " " : ( b < B10 ) ? b : ( b == B10 ) ? "0" : (""+(char)(54+b))) ); System.out.println("");
 		o = B_1; while ( ++o <= start ) System.out.print(">"); --o; while ( ++o < end ) System.out.print(" ");  --o; while ( ++o < lgt ) System.out.print("<"); 
 		System.out.println(""); System.out.println("");
-	    }	
+	    }
 	    fout.close();
 	    System.out.println("[" + String.format(Locale.US, "%02d", new Long((cur=(System.currentTimeMillis()-t)/1000)/60))
 			       + ":" + (line="0"+(cur%60)).substring(line.length()-2) + "]" 
 			       + String.format(Locale.US, "%,12d", new Integer(pcpt)) + " reads processed:" 
 			       + String.format(Locale.US, "%,12d", new Integer(ftcpt)) + " trimmed" 
 			       + String.format(Locale.US, "%,12d", new Integer(frcpt)) + " removed");
-	}
+	} 
+
 
 
 
@@ -961,12 +974,20 @@ public class AlienTrimmer {
 	    //################################
 	    //## trimming reads (fwd & rev) ##
 	    //################################
-	    fin = new BufferedReader(new FileReader(finfile)); fout = new BufferedWriter(new FileWriter(foutfile));
-	    rin = new BufferedReader(new FileReader(rinfile)); rout = new BufferedWriter(new FileWriter(routfile));
+      if(finext.equals("gz") || finext.equals(".gzip")) fin = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(finfile))));
+      else fin = new BufferedReader(new FileReader(finfile));
+      if(foutext.equals("gz") || foutext.equals(".gzip")) fout = new BufferedWriter(new OutputStreamWriter(new GZIPOutputStream(new FileOutputStream(foutfile))));
+      else fout = new BufferedWriter(new FileWriter(foutfile));
+      if(rinext.equals("gz") || rinext.equals(".gzip")) rin = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(rinfile))));
+      else rin = new BufferedReader(new FileReader(rinfile));
+      if(routext.equals("gz") || routext.equals(".gzip")) rout = new BufferedWriter(new OutputStreamWriter(new GZIPOutputStream(new FileOutputStream(routfile))));
+      else rout = new BufferedWriter(new FileWriter(routfile));
+	    //fin = new BufferedReader(new FileReader(finfile)); fout = new BufferedWriter(new FileWriter(foutfile));
+	    //rin = new BufferedReader(new FileReader(rinfile)); rout = new BufferedWriter(new FileWriter(routfile));
 	    sout = new BufferedWriter(new FileWriter(soutfile));
 	    pcpt = 0; ftcpt = 0; rtcpt = 0; rtcpt = 0; rrcpt = 0;
 	    cpt = B0; score = new byte[51];
-	    while ( true ) {
+      while ( true ) {
 		//## reading fastq ##
 		try { line = fin.readLine().trim(); } catch ( NullPointerException e ) { fin.close(); rin.close(); break; }
 		switch ( ++cpt ) { case B1: fid1 = line; break; case B2: fseq = line.toUpperCase(); break; case B3: fid2 = line; break; case B4: fqsc = line; break; }