Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Launch files refactor #67

Open
wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Launch files refactor #67

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
131 changes: 47 additions & 84 deletions src/org/usadellab/trimmomatic/Pairomatic.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,122 +10,95 @@
import org.usadellab.trimmomatic.fastq.FastqRecord;
import org.usadellab.trimmomatic.fastq.FastqSerializer;

public class Pairomatic
{
public class Pairomatic {

/**
* Pairomatic: The FASTQ pair/unpairer
*/

public Pairomatic()
{
public Pairomatic() {}

}

private Set<String> getFastqNames(File file, Character delimiter) throws IOException
{
private Set<String> getFastqNames(File file, Character delimiter) throws IOException {
Set<String> names = new LinkedHashSet<String>();

FastqParser parser = new FastqParser(0);
parser.open(file);

while (parser.hasNext())
{
while (parser.hasNext()) {
FastqRecord rec = parser.next();

String name = rec.getName();

if (delimiter != null)
{
if (delimiter != null) {
int index = name.lastIndexOf(delimiter);

if (index == -1)
throw new RuntimeException("Error: Failed to find expected delimiter '" + delimiter
+ "' in record named '" + name + "'");

name = name.substring(0, index);
}
}

if(names.contains(name))
throw new RuntimeException("Error: Found "+name+" more than once in file - check delimiter is correct '"+delimiter+"'");
throw new RuntimeException("Error: Found " + name + " more than once in file - check delimiter is correct '" + delimiter + "'");

names.add(name);
}
}

return names;
}


private boolean equalOrdering(Set<String> set1, Set<String> set2)
{
if(set1.size()!=set2.size())
return false;
private boolean equalOrdering(Set<String> set1, Set<String> set2) {
if(set1.size() != set2.size()) return false;

Iterator<String> iter1=set1.iterator();
Iterator<String> iter2=set2.iterator();
Iterator<String> iter1 = set1.iterator();
Iterator<String> iter2 = set2.iterator();

while(iter1.hasNext() && iter2.hasNext())
{
String str1=iter1.next();
String str2=iter2.next();
while(iter1.hasNext() && iter2.hasNext()) {
String str1 = iter1.next();
String str2 = iter2.next();

if(!str1.equals(str2))
return false;
}

if(iter1.hasNext())
return false;

if(iter2.hasNext())
return false;

return true;
}
if(!str1.equals(str2)) return false;
}

return !iter1.hasNext() && !iter2.hasNext();
}


private void splitFastq(File input, File match, File unmatch, Set<String> toKeep, Character delimiter)
throws IOException
{
private void splitFastq(File input, File match, File unmatch, Set<String> toKeep, Character delimiter) throws IOException {
FastqParser parser = new FastqParser(0);
parser.open(input);

FastqSerializer matchSerializer=new FastqSerializer();
FastqSerializer matchSerializer = new FastqSerializer();
matchSerializer.open(match);

FastqSerializer unmatchSerializer=new FastqSerializer();
FastqSerializer unmatchSerializer = new FastqSerializer();
unmatchSerializer.open(unmatch);

while (parser.hasNext())
{
while (parser.hasNext()) {
FastqRecord rec = parser.next();

String name = rec.getName();

if (delimiter != null)
{
if (delimiter != null) {
int index = name.indexOf(delimiter);

if (index == -1)
throw new RuntimeException("Failed to find expected delimiter '" + delimiter
+ "' in record named '" + name + "'");

name = name.substring(0, index);
}

if(toKeep.contains(name))
matchSerializer.writeRecord(rec);
else
unmatchSerializer.writeRecord(rec);
}

if(toKeep.contains(name)) matchSerializer.writeRecord(rec);
else unmatchSerializer.writeRecord(rec);
}

matchSerializer.close();
unmatchSerializer.close();

}

public void process(File input1, File input2, File output1P, File output1U, File output2P, File output2U,
Character delimiter) throws IOException
{
public void process(File input1, File input2, File output1P, File output1U,
File output2P, File output2U, Character delimiter) throws IOException {
Set<String> names1 = getFastqNames(input1, delimiter);
System.err.println("First input file contains " + names1.size() + " records");

Expand All @@ -136,11 +109,10 @@ public void process(File input1, File input2, File output1P, File output1U, File
System.err.println("Files shared " + names1.size() + " records");

names2.retainAll(names1);
if(!equalOrdering(names1,names2))
{
if(!equalOrdering(names1, names2)) {
System.err.println("Error: Common records are not in identical order, cowardly refusing to do anything");
return;
}
}

System.err.println("Splitting first file");
splitFastq(input1, output1P, output1U, names1, delimiter);
Expand All @@ -151,38 +123,30 @@ public void process(File input1, File input2, File output1P, File output1U, File
System.err.println("All done");
}

public static void main(String[] args) throws IOException
{
public static void main(String[] args) throws IOException {
int argIndex = 0;
Character delim=null;

Character delim = null;
boolean badOption = false;

while (argIndex < args.length && args[argIndex].startsWith("-"))
{
while (argIndex < args.length && args[argIndex].startsWith("-")) {
String arg = args[argIndex++];
if(arg.equals("-delim"))
{
String delimStr=args[argIndex++];
if(arg.equals("-delim")) {
String delimStr = args[argIndex++];

if(delimStr.length()!=1)
System.err.println("Delimiter must be exactly one character, got '"+delimStr+"'");
else
delim=delimStr.charAt(0);
}
else
{
if(delimStr.length()!=1) System.err.println("Delimiter must be exactly one character, got '" + delimStr + "'");
else delim = delimStr.charAt(0);
} else {
System.err.println("Unknown option " + arg);
badOption = true;
}
}
}

if (args.length - argIndex < 6 || badOption)
{
System.err
.println("Usage: Pairomatic [-delim delimChar] <inputFile1> <inputFile2> <outputFile1P> <outputFile1U> <outputFile2P> <outputFile2U>");
if (args.length - argIndex < 6 || badOption) {
System.err.println("Usage: Pairomatic [-delim delimChar] " +
"<inputFile1> <inputFile2> <outputFile1P> <outputFile1U> " +
"<outputFile2P> <outputFile2U>");
System.exit(1);
}
}

File input1 = new File(args[argIndex++]);
File input2 = new File(args[argIndex++]);
Expand All @@ -195,6 +159,5 @@ public static void main(String[] args) throws IOException

Pairomatic pm = new Pairomatic();
pm.process(input1, input2, output1P, output1U, output2P, output2U, delim);

}
}
Loading