Merge pull request #88 from nh13/nh_add_ns_to_total_depth

Add an option to include Ns in the total depth

Author: SilinPavel

Readme.md

@@ -97,6 +97,8 @@ To run all integration tests, the command is:
 ./gradlew test --tests com.astrazeneca.vardict.integrationtests.IntegrationTest 
 ```
 
+The results of the tests can be viewed in the `build/reports/tests/index.html` file.
+
 ##### User extension of testcases
 
 Each file in `testdata/intergationtestcases` directory represents a test case with input data and expected output
@@ -196,6 +198,8 @@ The VarDictJava program follows the workflow:
     Indicate to remove duplicated reads.  Only one pair with identical start positions will be kept
 - `-3`   
      Indicate to move indels to 3-prime if alternative alignment can be achieved.
+- `-K`
+     Include Ns in the total depth calculation.
 - `-F bit`  
      The hexical to filter reads. Default: `0x500` (filter 2nd alignments and duplicates).  Use `-F 0` to turn it off.
 - `-z 0/1`       

VarDict

@@ -120,11 +120,11 @@ public class Configuration {
      */
     double qratio = 1.5; //-o
     /**
-     * The minimun mean mapping quality to be considered
+     * The minimum mean mapping quality to be considered
      */
     double mapq = 0; // -O  default 0
     /**
-     * Do pileup regarless the frequency
+     * Do pileup regardless the frequency
      */
     boolean doPileup = false; // -p
     /**
@@ -137,7 +137,11 @@ public class Configuration {
     boolean outputSplicing = false; // -i Output splicing read counts
 
     ValidationStringency validationStringency = ValidationStringency.LENIENT;
-
+    
+    /**
+     * Include Ns in the total depth calculation.
+     */
+    boolean includeNInTotalDepth = false; // -K
 
 
     /**
@@ -194,4 +198,4 @@ public String getBamRaw() {
 
     }
 
-}
+}

src/main/java/com/astrazeneca/vardict/Configuration.java

@@ -128,6 +128,10 @@ private void run(CommandLine cmd) throws ParseException, IOException {
         if (cmd.hasOption("VS")) {
             conf.validationStringency = ValidationStringency.valueOf(cmd.getParsedOptionValue("VS").toString().toUpperCase());
         }
+        
+        if (cmd.hasOption("K")) {
+            conf.includeNInTotalDepth = true;
+        }
 
         conf.threads = Math.max(readThreadsCount(cmd), 1);
 
@@ -176,7 +180,7 @@ private static Options buildOptions() {
 //        options.addOption("M", false, "Similar to -D, but will append individual quality and position data instead of mean");
         options.addOption("t", false, "Indicate to remove duplicated reads.  Only one pair with same start positions will be kept");
         options.addOption("3", false, "Indicate to move indels to 3-prime if alternative alignment can be achieved.");
-
+        options.addOption("K", false, "Include Ns in the total depth calculation");
 
         options.addOption(OptionBuilder.withArgName("bit")
                 .hasArg(true)

src/main/java/com/astrazeneca/vardict/Main.java

@@ -1380,6 +1380,7 @@ public void close() throws IOException {
      * @throws IOException
      */
     static Tuple4<Map<Integer, Map<String, Variation>>, Map<Integer, Map<String, Variation>>, Map<Integer, Integer>, Integer> parseSAM(Region region, String bam,
+ 
             Map<String, Integer> chrs, String sample, Set<String> splice, String ampliconBasedCalling, int rlen, Map<Integer, Character> ref, Configuration conf) throws IOException {
 
         String[] bams = bam.split(":");
@@ -2228,6 +2229,9 @@ && isHasAndEquals(querySequence.charAt(n - 1), ref, start - 1)) {
                             boolean startWithDelition = false;
                             //skip if base is unknown
                             if (ch1 == 'N') {
+                                if (conf.includeNInTotalDepth) {
+                                    incCnt(cov, start, 1);
+                                }
                                 start++;
                                 n++;
                                 p++;

src/main/java/com/astrazeneca/vardict/VarDict.java

@@ -0,0 +1 @@
+chr1,390320,392323,GACTAGACGGTTGGCTAATACTTCAGAGCTTGCAGAGCATCTTTATACACTTTTAATCCTCCTAACAACCGTGAGAGATGGAGCTTACTATTATCATCCGTGTTTGCAAATGAGGCCCTGAGAAGTTGAGTGATTTCTGTAAGGTCTCAGAGCCAATAGACACTGGTAATGAAATAAAATGCAAGGCCCCTTATCTTTGGAGCCCAGTGTTCCTTCCACATAGGTGGTTCTCCACCCAGGCTGCCCAGGAGAATGTGGAATCTCCAGCAGTTCTGACTTAACTGGCCTGGTGTGGATGTCTGTGATGGGTGAACATTCCCAGACCCTTTTAAGAACGTGATAGAAGTGGTAGACCCACTTCCCAGAAAAAGGGACGCACAACAAAATAATTGTCCTGAGTGGGTCTGACAGAATCAAGTGAACCCTTTAAATCTGGATCTAGAGGTCAGAGACTGAGAATGTCAGAGATGCAAAAGAGATTCAGTGCAAGAGAAATCCTCCTACTGGTTTTGAAGATAGATGTTGGCACCCTGTGTCAACAACCTGAGAGTGGCCTTGAGTTGCTGGGAGCACCCCAGACTGACAAACAGCAAGAAGAATATGGGGACCTCAGTCCTACAACCACAGGAACTGAATTCTACTGACAACCAGTGAGCTTGCAAAGAGGACTTGGAGCCCCAGATGAGAAGCAACCCTGGCTACCCCGATCTCAACCCTGTGAGATCCTAAACAGACAATCCAGCCATGCAACACCCAAACTTCTGACCTATAGAAACCCTGAGATAATAAATGGGCATTGCTCTAAATCACCAAGTTTGTGGTAATTTGTTACACAGCCATAGGAAGTGAATCGACCCGATGTATCTGAGCACCTGCTAGGTTATCATTAAGATTACTCTTCAAAGGTAAAAATTATTTTTCAAAATGTTTCTGCCCTACCTTCCGTGAGCATCTGGTGATGGATGGACACACACACATAAAGGTAGACTGTGTTTAGGTGGGCATGGTGGTGCATACCTGTGGTCCCAGCTACTCAGGAGGCTGAAAGAGGAGGATCACTAGGGCCCAGGAGTTCAAGGCTGCAGTGAAGCTGTGATTGAGCCATTGCACTCAAACTTGGGCAACAGAGCAAGACACCAGCTCTAAAAAAAAAAAAAACTGCTGAATGCTATAAATAAGATTGGAACTTGCTCTGCTTTTACAAGACCACTGTTAGATGACCACTGACAAGAAGACTGTGAGCTGGTCTCTGTAGGAAGCAGGGGCCTGGGCAGCTCTGGGGGCACAGGAGACAGGCCTGGGGCAGAGACACCTCAGGGCATTTTCAGAAGACAGCCAAAGCAGCCATTCCAGCTTGTCCAGGTAGATGGCAAGTCAATGGGAAATGATTCCAGGAAGGTAGGGAAAGATGGAATTCTGGAGAGCATTGGACCTCAGATTGGGAGTCTGAACGTCTTTCCATATGCATCAGGAAGCCATGGAAAATTCACAGACTGGAGTGACTTTGGCAAAGGTGGGATTTAGGAAGACTGATCAAGGCACGGGATAGACCCATGGATGAATAGCCTTCTGGTCAGTTTGTCCCTGTGGTTTTCTATGCTGAGGAGGTGGGAATGTGCTGGGTGAGTCAGCTGTGGATTTGTGTCCCTGCCTCACCTCACTCCCCACTGTCGTGGATTTGTCGGCTCATCTTTAGTGCGCTCCCTGAAGAAACACTCAGTTCACTCAGCTTGTTTCTAACCCAAAACACTCTGCAGGGCCCATCCTCTTGTCTTTGCCTGGGGATGCCAGACCATGCACTGCGGATGCCTTCCGCCTTAGCACTAGTGGGCTAAATGATGACTGCCTTGCTGTCCCAACACCACCCATCAAAGGGAAGACATCACCACTGGGGTCAGTACAGCCCAAGTGACAAACTCTATTCCCTCCTTTCTCTCCATCCCATGGACCCTTGATTTGCTAAGTGGGAAGACACTTTCTCGTGGTTCAACATCACCTAATCTG

src/test/resources/com/astrazeneca/vardict/integrationtests/Count-Depth-With-Ns.bam

@@ -0,0 +1,24 @@
+Simple,hs38DH.fa,Count-Depth-With-Ns.bam,chr1,391310,391333,-K -p -r 1 -q 2 -f 0.0
+Count-Depth-With-Ns	testbed	chr1	391311	391311			0	0	0	0	0	0		0	0;0	0	0	0	0	0		0	0	0	0	0	0			0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391312	391312			0	0	0	0	0	0		0	0;0	0	0	0	0	0		0	0	0	0	0	0			0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391313	391313			0	0	0	0	0	0		0	0;0	0	0	0	0	0		0	0	0	0	0	0			0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391314	391314			0	0	0	0	0	0		0	0;0	0	0	0	0	0		0	0	0	0	0	0			0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391315	391315			0	0	0	0	0	0		0	0;0	0	0	0	0	0		0	0	0	0	0	0			0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391316	391316			0	0	0	0	0	0		0	0;0	0	0	0	0	0		0	0	0	0	0	0			0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391317	391317			0	0	0	0	0	0		0	0;0	0	0	0	0	0		0	0	0	0	0	0			0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391318	391318			0	0	0	0	0	0		0	0;0	0	0	0	0	0		0	0	0	0	0	0			0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391319	391319			0	0	0	0	0	0		0	0;0	0	0	0	0	0		0	0	0	0	0	0			0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391320	391320			0	0	0	0	0	0		0	0;0	0	0	0	0	0		0	0	0	0	0	0			0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391321	391321	G	C	3	1	0	1	0	1	G/C	0.3333	0;0	1.0	0	27.0	0	0.0	2.000	0.5000	0	0	1.000	1	0.0	1	2	GGTAGACTGTGTTTAGGTGG	CATGGTGGTGCATACCTGTG	chr1:391311-391333	SNV
+Count-Depth-With-Ns	testbed	chr1	391322	391322	C	G	3	1	0	2	0	1	C/G	0.3333	0;0	2.0	0	36.0	0	0.0	2.000	0.3333	0	0	1.000	1	0.0	1	3	GTAGACTGTGTTTAGGTGGG	ATGGTGGTGCATACCTGTGG	chr1:391311-391333	SNV
+Count-Depth-With-Ns	testbed	chr1	391323	391323	A	A	3	0	0	3	0	0	A/A	0.0000	0;0	3.0	0	36.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391324	391324	T	T	3	0	0	3	0	0	T/T	0.0000	0;0	4.0	0	36.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391325	391325	G	G	3	0	0	3	0	0	G/G	0.0000	0;0	5.0	0	36.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391326	391326	G	G	3	0	0	3	0	0	G/G	0.0000	0;0	6.0	0	36.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391327	391327	T	T	3	0	0	3	0	0	T/T	0.0000	0;0	7.0	0	14.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391328	391328	G	G	3	0	0	3	0	0	G/G	0.0000	0;0	8.0	0	36.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391329	391329	G	G	3	0	0	3	0	0	G/G	0.0000	0;0	9.0	0	36.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391330	391330	T	T	3	0	0	3	0	0	T/T	0.0000	0;0	10.0	0	32.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391331	391331	G	G	3	0	0	3	0	0	G/G	0.0000	0;0	11.0	0	36.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391332	391332	C	C	3	0	0	3	0	0	C/C	0.0000	0;0	12.0	0	36.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391333	391333	A	A	3	0	0	3	0	0	A/A	0.0000	0;0	13.0	0	36.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333	

src/test/resources/com/astrazeneca/vardict/integrationtests/Count-Depth-With-Ns.bam.bai

@@ -0,0 +1,24 @@
+Simple,hs38DH.fa,Count-Depth-With-Ns.bam,chr1,391310,391333,-p -r 1 -q 2 -f 0.0
+Count-Depth-With-Ns	testbed	chr1	391311	391311			0	0	0	0	0	0		0	0;0	0	0	0	0	0		0	0	0	0	0	0			0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391312	391312			0	0	0	0	0	0		0	0;0	0	0	0	0	0		0	0	0	0	0	0			0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391313	391313			0	0	0	0	0	0		0	0;0	0	0	0	0	0		0	0	0	0	0	0			0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391314	391314			0	0	0	0	0	0		0	0;0	0	0	0	0	0		0	0	0	0	0	0			0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391315	391315			0	0	0	0	0	0		0	0;0	0	0	0	0	0		0	0	0	0	0	0			0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391316	391316			0	0	0	0	0	0		0	0;0	0	0	0	0	0		0	0	0	0	0	0			0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391317	391317			0	0	0	0	0	0		0	0;0	0	0	0	0	0		0	0	0	0	0	0			0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391318	391318			0	0	0	0	0	0		0	0;0	0	0	0	0	0		0	0	0	0	0	0			0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391319	391319			0	0	0	0	0	0		0	0;0	0	0	0	0	0		0	0	0	0	0	0			0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391320	391320			0	0	0	0	0	0		0	0;0	0	0	0	0	0		0	0	0	0	0	0			0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391321	391321	G	C	2	1	0	1	0	1	G/C	0.5000	0;0	1.0	0	27.0	0	0.0	2.000	0.5000	0	0	1.000	1	0.0	1	2	GGTAGACTGTGTTTAGGTGG	CATGGTGGTGCATACCTGTG	chr1:391311-391333	SNV
+Count-Depth-With-Ns	testbed	chr1	391322	391322	C	G	3	1	0	2	0	1	C/G	0.3333	0;0	2.0	0	36.0	0	0.0	2.000	0.3333	0	0	1.000	1	0.0	1	3	GTAGACTGTGTTTAGGTGGG	ATGGTGGTGCATACCTGTGG	chr1:391311-391333	SNV
+Count-Depth-With-Ns	testbed	chr1	391323	391323	A	A	3	0	0	3	0	0	A/A	0.0000	0;0	3.0	0	36.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391324	391324	T	T	3	0	0	3	0	0	T/T	0.0000	0;0	4.0	0	36.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391325	391325	G	G	3	0	0	3	0	0	G/G	0.0000	0;0	5.0	0	36.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391326	391326	G	G	3	0	0	3	0	0	G/G	0.0000	0;0	6.0	0	36.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391327	391327	T	T	3	0	0	3	0	0	T/T	0.0000	0;0	7.0	0	14.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391328	391328	G	G	3	0	0	3	0	0	G/G	0.0000	0;0	8.0	0	36.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391329	391329	G	G	3	0	0	3	0	0	G/G	0.0000	0;0	9.0	0	36.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391330	391330	T	T	3	0	0	3	0	0	T/T	0.0000	0;0	10.0	0	32.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391331	391331	G	G	3	0	0	3	0	0	G/G	0.0000	0;0	11.0	0	36.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391332	391332	C	C	3	0	0	3	0	0	C/C	0.0000	0;0	12.0	0	36.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333	
+Count-Depth-With-Ns	testbed	chr1	391333	391333	A	A	3	0	0	3	0	0	A/A	0.0000	0;0	13.0	0	36.0	0	0.0	6.000	1.0000	0	0	0	0	0.0	3	3	0	0	chr1:391311-391333