new --unmapped option in sambamba view

Author: lomereiter

BioD

@@ -30,7 +30,7 @@ import sambamba.utils.common.ldc_gc_workaround;
 import std.stdio;
 
 void printUsage() {
-    stderr.writeln("sambamba v0.4.1");
+    stderr.writeln("sambamba v0.4.2");
     stderr.writeln();
     stderr.writeln("Usage: sambamba [command] [args...]");
     stderr.writeln();

main.d

@@ -59,6 +59,8 @@ void printUsage() {
     stderr.writeln("                    output to stdout only reference names and lengths in JSON");
     stderr.writeln("         -c, --count");
     stderr.writeln("                    output to stdout only count of matching records, hHI are ignored");
+    stderr.writeln("         -U, --unmapped");
+    stderr.writeln("                    output reads with RNAME = *; available for indexed BAM only");
     stderr.writeln("         -v, --valid");
     stderr.writeln("                    output only valid alignments");
     stderr.writeln("         -S, --sam-input");
@@ -105,6 +107,7 @@ bool with_header;
 bool header_only;
 bool reference_info_only;
 bool count_only;
+bool unmapped_only;
 bool skip_invalid_alignments;
 bool is_sam;
 
@@ -137,6 +140,7 @@ int view_main(string[] args) {
                "header|H",            &header_only,
                "reference-info|I",    &reference_info_only,
                "count|c",             &count_only,
+               "unmapped|U",          &unmapped_only,
                "valid|v",             &skip_invalid_alignments,
                "sam-input|S",         &is_sam,
                "show-progress|p",     &show_progress,
@@ -198,6 +202,18 @@ int sambambaMain(T)(T _bam, TaskPool pool, string[] args)
         return 0;
     }
 
+    static if (is(T == SamReader)) {
+        if (unmapped_only) {
+            stderr.writeln("--unmapped option is available only for indexed BAMs");
+            return -1;
+        }
+    }
+
+    if (unmapped_only && args.length > 2) {
+        stderr.writeln("--unmapped option can't be used together with regions");
+        return -1;
+    }
+
     if (header_only && !count_only) {
         // write header to stdout
         (new HeaderSerializer(stdout, format)).writeln(bam.header);
@@ -255,7 +271,10 @@ int sambambaMain(T)(T _bam, TaskPool pool, string[] args)
                     runProcessor(bam, reads, read_filter);
                     bar.finish();
                 } else {
-                    runProcessor(bam, bam.reads!withoutOffsets(), read_filter);
+                    if (unmapped_only)
+                        runProcessor(bam, bam.unmappedReads(), read_filter);
+                    else
+                        runProcessor(bam, bam.reads!withoutOffsets(), read_filter);
                 }
             } else { // SamFile
                 runProcessor(bam, bam.reads, read_filter);