Merge pull request #25 from Integrative-Transcriptomics/development

Development

src/main/java/IO/Communicator.java

@@ -13,9 +13,11 @@ public class Communicator {
 
     // damage calculation
     private int threshold = 25;
+
     private double yAxis;
     private int length = 100;
-    private boolean use_merged_and_mapped_reads = true;
+    private boolean use_merged_and_mapped_reads = false;
+    private boolean use_all_reads = false;
 
     // specie filtering
     private String species_ref_identifier = null;
@@ -24,26 +26,6 @@ public class Communicator {
     private String title_plots;
 
 
-//
-//    // options recsaling
-//    private boolean perform_rescaling = false;
-//
-//    private int rand = 30;          // Number of random starting points for the likelihood optimization
-//    private int burn = 10000;       // Number of burnin iterations
-//    private int adjust = 10;        // Number of adjust proposal variance parameters iterations
-//    private int iter = 50000;       // Number of final MCMC iterations
-//    private boolean forward = false;  // Using only the 5' end of the seqs
-//    private boolean reverse = false;  // Using only the 3' end of the seqs
-//    private boolean var_disp = false; // Variable dispersion in the overhangs
-//    private boolean jukes_cantor = false;  // Use Jukes Cantor instead of HKY85
-//    private boolean diff_hangs = false; // The overhangs are different for 5' and 3'
-//    private int nu_samples = 0;
-//    private boolean fix_nicks = false; // Fix the nick frequency vector (Only C.T from the 5' end and G.A from the 3' end)
-//    private boolean use_raw_nick_freq = false; // Use the raw nick frequency vector without smoothing
-//    private boolean single_stranded = false;  // Single stranded protocol
-//    private int seq_length = 12; // how long sequence to use from each side
-//    private int minQual = 0;
-
 
     public Communicator(){
 
@@ -105,6 +87,14 @@ public void setUse_merged_and_mapped_reads(boolean use_merged_and_mapped_reads)
         this.use_merged_and_mapped_reads = use_merged_and_mapped_reads;
     }
 
+    public boolean isUse_all_reads() {
+        return use_all_reads;
+    }
+
+    public void setUse_all_reads(boolean use_all_reads) {
+        this.use_all_reads = use_all_reads;
+    }
+
     public void setyAxis(double yAxis) {
         this.yAxis = yAxis;
     }
@@ -130,134 +120,5 @@ public void setSpecieslist_filepath(String specieslist_filepath) {
     }
 
 
-//    public boolean isPerform_rescaling() {
-//        return perform_rescaling;
-//    }
-//
-//    public void setPerform_rescaling(boolean perform_rescaling) {
-//        this.perform_rescaling = perform_rescaling;
-//    }
-//
-//
-//    public int getRand() {
-//        return rand;
-//    }
-//
-//    public void setRand(int rand) {
-//        this.rand = rand;
-//    }
-//
-//    public int getBurn() {
-//        return burn;
-//    }
-//
-//    public void setBurn(int burn) {
-//        this.burn = burn;
-//    }
-//
-//    public int getAdjust() {
-//        return adjust;
-//    }
-//
-//    public void setAdjust(int adjust) {
-//        this.adjust = adjust;
-//    }
-//
-//    public int getIter() {
-//        return iter;
-//    }
-//
-//    public void setIter(int iter) {
-//        this.iter = iter;
-//    }
-//
-//    public boolean isForward() {
-//        return forward;
-//    }
-//
-//    public void setForward(boolean forward) {
-//        this.forward = forward;
-//    }
-//
-//    public boolean isReverse() {
-//        return reverse;
-//    }
-//
-//    public void setReverse(boolean reverse) {
-//        this.reverse = reverse;
-//    }
-//
-//    public boolean isVar_disp() {
-//        return var_disp;
-//    }
-//
-//    public void setVar_disp(boolean var_disp) {
-//        this.var_disp = var_disp;
-//    }
-//
-//    public boolean isJukes_cantor() {
-//        return jukes_cantor;
-//    }
-//
-//    public void setJukes_cantor(boolean jukes_cantor) {
-//        this.jukes_cantor = jukes_cantor;
-//    }
-//
-//    public boolean isDiff_hangs() {
-//        return diff_hangs;
-//    }
-//
-//    public void setDiff_hangs(boolean diff_hangs) {
-//        this.diff_hangs = diff_hangs;
-//    }
-//
-//    public int getNu_samples() {
-//        return nu_samples;
-//    }
-//
-//    public void setNu_samples(int nu_samples) {
-//        this.nu_samples = nu_samples;
-//    }
-//
-//    public boolean isFix_nicks() {
-//        return fix_nicks;
-//    }
-//
-//    public void setFix_nicks(boolean fix_nicks) {
-//        this.fix_nicks = fix_nicks;
-//    }
-//
-//    public boolean isUse_raw_nick_freq() {
-//        return use_raw_nick_freq;
-//    }
-//
-//    public void setUse_raw_nick_freq(boolean use_raw_nick_freq) {
-//        this.use_raw_nick_freq = use_raw_nick_freq;
-//    }
-//
-//    public boolean isSingle_stranded() {
-//        return single_stranded;
-//    }
-//
-//    public void setSingle_stranded(boolean single_stranded) {
-//        this.single_stranded = single_stranded;
-//    }
-//
-//    public int getSeq_length() {
-//        return seq_length;
-//    }
-//
-//    public void setSeq_length(int seq_length) {
-//        this.seq_length = seq_length;
-//    }
-//
-//    public int getMinQual() {
-//        return minQual;
-//    }
-//
-//    public void setMinQual(int minQual) {
-//        this.minQual = minQual;
-//    }
-
 
 }

src/main/java/IO/UserOptionsParser.java

@@ -76,78 +76,14 @@ private void parse(){
                 .create("yaxis"));
 
 
-        Option mapped_and_merged = new Option("mapped", "all_mapped_reads", false,
-                "Use all mapped reads to calculate damage plots. Default: false ");
+        Option mapped_and_merged = new Option("merged", "all_mapped_and_merged_reads", false,
+                "Use all mapped and merged reads to calculate damage plot instead of using all mapped reads. The SAM/BAM entry must start with 'M_', otherwise " +
+                        " it will be skipped. Default: false ");
         options.addOption(mapped_and_merged);
 
-
-//        // recsaling options
-//        Option rescaling = new Option("rescale", "Rescaling_misincorporations", false,
-//                "Correct the damaged bases and generate new BAM file.");
-//        options.addOption(rescaling);
-//        options.addOption(OptionBuilder.withLongOpt("rand")
-//                .withArgName("RAND")
-//                .withDescription("Number of random starting points for the likelihood optimization")
-//                .hasArg()
-//                .create("rand"));
-//        options.addOption(OptionBuilder.withLongOpt("burn")
-//                .withArgName("BURN")
-//                .withDescription("Number of burnin iterations ")
-//                .hasArg()
-//                .create("burn"));
-//        options.addOption(OptionBuilder.withLongOpt("adjust")
-//                .withArgName("ADJUST")
-//                .withDescription("Number of adjust proposal variance parameters iterations.")
-//                .hasArg()
-//                .create("adjust"));
-//        options.addOption(OptionBuilder.withLongOpt("iter")
-//                .withArgName("Iterations")
-//                .withDescription("Number of final MCMC iterations")
-//                .hasArg()
-//                .create("iter"));
-//        options.addOption(OptionBuilder.withLongOpt("Q")
-//                .withArgName("MINQUALITY")
-//                .withDescription("Minimal base quality Phred score considered")
-//                .hasArg()
-//                .create("Q"));
-//        options.addOption(OptionBuilder.withLongOpt("seq_length")
-//                .withArgName("SEQ_LENGTH")
-//                .withDescription("How long sequence to use from each side by considering the damage probabilities. Default: 12")
-//                .hasArg()
-//                .create("seq_length"));
-//
-//        Option only_forward = new Option("forward", "only_forward", false,
-//                "Using only forward reads (5' end). Default: false");
-//        options.addOption(only_forward);
-//
-//        Option only_reverse = new Option("reverse", "only_reverse", false,
-//                "Using only reverse reads (3' end). Default: false");
-//        options.addOption(only_reverse);
-//
-//        Option var_disp_opt = new Option("var_disp", "var_disp", false,
-//                "Variable dispersion in the overhangs . Default: false");
-//        options.addOption(var_disp_opt);
-//
-//        Option jukes_cantor_opt = new Option("jukes_cantor", "jukes_cantor", false,
-//                "Use Jukes Cantor transition matrix instead of HKY85. Default: false");
-//        options.addOption(jukes_cantor_opt);
-//
-//        Option diff_hangs_opt = new Option("diff_hangs", "diff_hangs", false,
-//                "The overhangs are different for 5' and 3'. Default: false");
-//        options.addOption(diff_hangs_opt);
-//
-//        Option fix_nicks_opt = new Option("fix_nicks", "fix_nicks", false,
-//                "Fix the nick frequency vector (Only C>T from the 5' end and G>A from the 3' end). Default: false");
-//        options.addOption(fix_nicks_opt);
-//
-//        Option use_raw_nick_freq_opt = new Option("use_raw_nick_freq", "use_raw_nick_freq", false,
-//                "Use the raw nick frequency vector without smoothing. Default: false");
-//        options.addOption(use_raw_nick_freq_opt);
-//
-//        Option single_stranded_opt = new Option("single_stranded", "single_stranded", false,
-//                "Use Single stranded protocol. Default: false");
-//        options.addOption(single_stranded_opt);
-//
+        Option use_all_reads = new Option("useall", "use_all_reads", false,
+                "Use all reads (mapped and unmapped) to calculate damage plot. Default: false ");
+        options.addOption(use_all_reads);
 
 
         HelpFormatter helpformatter = new HelpFormatter();
@@ -194,8 +130,12 @@ private void parse(){
             if (cmd.hasOption('l')) {
                 communicator.setLength(Integer.parseInt(cmd.getOptionValue('l')));
             }
-            if(cmd.hasOption("all_mapped_reads")) {
-                communicator.setUse_merged_and_mapped_reads(false);
+            if(cmd.hasOption("all_mapped_and_merged_reads")) {
+                communicator.setUse_merged_and_mapped_reads(true);
+            }
+
+            if(cmd.hasOption("use_all_reads")) {
+                communicator.setUse_all_reads(false);
             }
 
             // Plotting
@@ -212,56 +152,6 @@ private void parse(){
                 communicator.setThreshold(Integer.parseInt(cmd.getOptionValue('t')));
             }
 
-//
-//            // options for rescaling
-//
-//            if(cmd.hasOption("Rescaling_misincorporations")) {
-//                communicator.setPerform_rescaling(true);
-//            }
-//
-//            if(cmd.hasOption("rand")) {
-//                communicator.setRand(Integer.parseInt(cmd.getOptionValue("rand")));
-//            }
-//            if(cmd.hasOption("burn")) {
-//                communicator.setBurn(Integer.parseInt(cmd.getOptionValue("burn")));
-//            }
-//            if(cmd.hasOption("adjust")) {
-//                communicator.setAdjust(Integer.parseInt(cmd.getOptionValue("adjust")));
-//            }
-//            if(cmd.hasOption("iter")) {
-//                communicator.setIter(Integer.parseInt(cmd.getOptionValue("iter")));
-//            }
-//            if(cmd.hasOption("only_forward")) {
-//                communicator.setForward(true);
-//            }
-//            if(cmd.hasOption("only_reverse")) {
-//                communicator.setReverse(true);
-//            }
-//            if(cmd.hasOption("var_disp")) {
-//                communicator.setVar_disp(true);
-//            }
-//            if(cmd.hasOption("jukes_cantor")) {
-//                communicator.setJukes_cantor(true);
-//            }
-//            if(cmd.hasOption("diff_hangs")) {
-//                communicator.setDiff_hangs(true);
-//            }
-//            if(cmd.hasOption("fix_nicks")) {
-//                communicator.setFix_nicks(true);
-//            }
-//            if(cmd.hasOption("use_raw_nick_freq")) {
-//                communicator.setUse_raw_nick_freq(true);
-//            }
-//            if(cmd.hasOption("single_stranded")) {
-//                communicator.setSingle_stranded(false);
-//            }
-//            if(cmd.hasOption("seq_length")) {
-//                communicator.setSeq_length(Integer.parseInt(cmd.getOptionValue("seq_length")));
-//            }
-//            if(cmd.hasOption('Q')) {
-//                communicator.setMinQual(Integer.parseInt(cmd.getOptionValue('Q')));
-//            }
-
 
         } catch (ParseException e) {
             helpformatter.printHelp(CLASS_NAME, options);