[index] optional output filename; closes #138

biod · May 16, 2015 · eafcf81 · eafcf81
1 parent 511fe52
commit eafcf81
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Showing 3 changed files with 21 additions and 8 deletions.
diff --git a/.test_suite.sh b/.test_suite.sh
@@ -57,4 +57,14 @@ testCramView() {
     assertEquals 0 $?
 }
 
+testIndexUsage() {
+    rm *.bai && rm c1_*
+    ./build/sambamba view -S htslib/test/c1\#pad2.sam -T htslib/test/c1.fa -f cram -o c1_pad2.cram &&
+    ./build/sambamba index -C c1_pad2.cram && test -e c1_pad2.cram.crai
+    ./build/sambamba index -C c1_pad2.cram c1_cram_index && test -e c1_cram_index.crai
+    ./build/sambamba index ex1_header.sorted.bam && test -e ex1_header.sorted.bam.bai
+    ./build/sambamba index ex1_header.sorted.bam ex1_header.sorted.bai && test -e ex1_header.sorted.bai
+    assertEquals 0 $?
+}
+
 . shunit2-2.0.3/src/shell/shunit2
diff --git a/cram/reader.d b/cram/reader.d
@@ -113,8 +113,8 @@ class CramReader : IBamSamReader {
         return inputRangeObject(reads());
     }
 
-    void createIndex() {
-        int ret = cram_index_build(_fd, toStringz(_fn));
+    void createIndex(string fn_prefix=null) {
+        int ret = cram_index_build(_fd, toStringz(fn_prefix is null ? _fn : fn_prefix));
         if (ret != 0) {
             throw new Exception("failed to build index for CRAM file " ~ _fn);
         }

diff --git a/sambamba/index.d b/sambamba/index.d
@@ -1,6 +1,6 @@
 /*
     This file is part of Sambamba.
-    Copyright (C) 2012-2013    Artem Tarasov <lomereiter@gmail.com>
+    Copyright (C) 2012-2015    Artem Tarasov <lomereiter@gmail.com>
 
     Sambamba is free software; you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
@@ -32,7 +32,7 @@ import bio.bam.bai.indexing;
 import bio.bam.reader;
 
 void printUsage() {
-    stderr.writeln("Usage: sambamba-index [OPTIONS] <input.bam|input.cram>");
+    stderr.writeln("Usage: sambamba-index [OPTIONS] <input.bam|input.cram> [output_file]");
     stderr.writeln();
     stderr.writeln("\tCreates index for a BAM or CRAM file");
     stderr.writeln();
@@ -58,6 +58,7 @@ int index_main(string[] args) {
     bool check_bins;
     uint n_threads = totalCPUs;
     bool is_cram;
+    string out_filename = null;
 
     getopt(args,
            std.getopt.config.caseSensitive,
@@ -67,14 +68,16 @@ int index_main(string[] args) {
            "cram-input|C",    &is_cram);
 
     try {
-        string out_filename = null;
-        if (args.length != 2) {
+        if (args.length < 2 || args.length > 3) {
             printUsage();
             return 0;
         }
 
         if (!is_cram) {
-            out_filename = args[1] ~ ".bai";
+            if (args.length > 2)
+                out_filename = args[2];
+            else
+                out_filename = args[1] ~ ".bai";
 
             // default taskPool uses only totalCPUs-1 threads,
             // but in case of indexing the most time is spent
@@ -103,7 +106,7 @@ int index_main(string[] args) {
                 stderr.writeln("[info] progressbar is unavailable for CRAM input");
             defaultPoolThreads = 0; // decompression not needed for CRAM
             auto cram = new CramReader(args[1], taskPool);
-            cram.createIndex();
+            cram.createIndex(args[$-1]);
         }
     } catch (Throwable e) {
         stderr.writeln("sambamba-index: ", e.msg);