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Fix TabularROD printing and testing so Aaron stops nagging me. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1016 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-06-16 15:49:26 +00:00
parent a0a549557f
commit 647b8a1ab0
2 changed files with 18 additions and 11 deletions
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12
java/src/org/broadinstitute/sting/gatk/refdata/TabularROD.java
View File

@ -196,8 +196,12 @@ public class TabularROD extends BasicReferenceOrderedDatum implements Map<String
// //
// ---------------------------------------------------------------------- // ----------------------------------------------------------------------
public GenomeLoc getLocation() { public GenomeLoc getLocation() {
loc = GenomeLoc.parseGenomeLoc(get(header.get(0))); if ( loc != null )
return loc; return loc;
String s = get(header.get(0));
if ( s == null )
return null;
return GenomeLoc.parseGenomeLoc(s);
} }
public ArrayList<String> getHeader() { public ArrayList<String> getHeader() {
@ -258,7 +262,9 @@ public class TabularROD extends BasicReferenceOrderedDatum implements Map<String
// //
// ---------------------------------------------------------------------- // ----------------------------------------------------------------------
public String toString() { public String toString() {
return String.format("%s\t%s", getLocation(), getAttributeString()); if ( loc != null )
return String.format("%s\t%s", loc, getAttributeString());
return String.format("%s", getAttributeString());
} }
/** /**

17
java/test/org/broadinstitute/sting/gatk/refdata/TabularRODTest.java
View File

@ -49,7 +49,7 @@ public class TabularRODTest extends BaseTest {
public void test1() { public void test1() {
logger.warn("Executing test1"); logger.warn("Executing test1");
TabularROD one = (TabularROD)iter.next(); TabularROD one = (TabularROD)iter.next();
assertTrue(one.size() == 3); assertTrue(one.size() == 4);
assertTrue(one.getLocation().equals(new GenomeLoc("chrM", 10))); assertTrue(one.getLocation().equals(new GenomeLoc("chrM", 10)));
assertTrue(one.get("COL1").equals("A")); assertTrue(one.get("COL1").equals("A"));
assertTrue(one.get("COL2").equals("B")); assertTrue(one.get("COL2").equals("B"));
@ -61,7 +61,7 @@ public class TabularRODTest extends BaseTest {
logger.warn("Executing test2"); logger.warn("Executing test2");
TabularROD one = (TabularROD)iter.next(); TabularROD one = (TabularROD)iter.next();
TabularROD two = (TabularROD)iter.next(); TabularROD two = (TabularROD)iter.next();
assertTrue(two.size() == 3); assertTrue(two.size() == 4);
assertTrue(two.getLocation().equals(new GenomeLoc("chrM", 20))); assertTrue(two.getLocation().equals(new GenomeLoc("chrM", 20)));
assertTrue(two.get("COL1").equals("C")); assertTrue(two.get("COL1").equals("C"));
assertTrue(two.get("COL2").equals("D")); assertTrue(two.get("COL2").equals("D"));
@ -74,7 +74,7 @@ public class TabularRODTest extends BaseTest {
TabularROD one = (TabularROD)iter.next(); TabularROD one = (TabularROD)iter.next();
TabularROD two = (TabularROD)iter.next(); TabularROD two = (TabularROD)iter.next();
TabularROD three = (TabularROD)iter.next(); TabularROD three = (TabularROD)iter.next();
assertTrue(three.size() == 3); assertTrue(three.size() == 4);
assertTrue(three.getLocation().equals(new GenomeLoc("chrM", 30))); assertTrue(three.getLocation().equals(new GenomeLoc("chrM", 30)));
assertTrue(three.get("COL1").equals("F")); assertTrue(three.get("COL1").equals("F"));
assertTrue(three.get("COL2").equals("G")); assertTrue(three.get("COL2").equals("G"));
@ -94,7 +94,7 @@ public class TabularRODTest extends BaseTest {
public void testSeek() { public void testSeek() {
logger.warn("Executing testSeek"); logger.warn("Executing testSeek");
TabularROD two = (TabularROD)iter.seekForward(new GenomeLoc("chrM", 20)); TabularROD two = (TabularROD)iter.seekForward(new GenomeLoc("chrM", 20));
assertTrue(two.size() == 3); assertTrue(two.size() == 4);
assertTrue(two.getLocation().equals(new GenomeLoc("chrM", 20))); assertTrue(two.getLocation().equals(new GenomeLoc("chrM", 20)));
assertTrue(two.get("COL1").equals("C")); assertTrue(two.get("COL1").equals("C"));
assertTrue(two.get("COL2").equals("D")); assertTrue(two.get("COL2").equals("D"));
@ -117,7 +117,7 @@ public class TabularRODTest extends BaseTest {
logger.warn("Executing testDelim1"); logger.warn("Executing testDelim1");
TabularROD one2 = (TabularROD)iter_commas.next(); TabularROD one2 = (TabularROD)iter_commas.next();
assertTrue(one2.size() == 4); assertTrue(one2.size() == 5);
assertTrue(one2.getLocation().equals(new GenomeLoc("chrM", 10))); assertTrue(one2.getLocation().equals(new GenomeLoc("chrM", 10)));
assertTrue(one2.get("COL1").equals("A")); assertTrue(one2.get("COL1").equals("A"));
assertTrue(one2.get("COL2").equals("B")); assertTrue(one2.get("COL2").equals("B"));
@ -134,7 +134,7 @@ public class TabularRODTest extends BaseTest {
logger.warn("Executing testDelim1"); logger.warn("Executing testDelim1");
TabularROD one2 = (TabularROD)iter_commas.next(); TabularROD one2 = (TabularROD)iter_commas.next();
assertTrue(one2.size() == 4); assertTrue(one2.size() == 5);
assertTrue(one2.getLocation().equals(new GenomeLoc("chrM", 10))); assertTrue(one2.getLocation().equals(new GenomeLoc("chrM", 10)));
assertTrue(one2.get("COL1").equals("A")); assertTrue(one2.get("COL1").equals("A"));
assertTrue(one2.get("COL2").equals("B")); assertTrue(one2.get("COL2").equals("B"));
@ -149,6 +149,7 @@ public class TabularRODTest extends BaseTest {
assertTrue(TabularROD.headerString(header).equals("HEADER\tcol1\tcol2\tcol3")); assertTrue(TabularROD.headerString(header).equals("HEADER\tcol1\tcol2\tcol3"));
String rowData = String.format("%d %d %d", 1, 2, 3); String rowData = String.format("%d %d %d", 1, 2, 3);
TabularROD row = new TabularROD("myName", header, new GenomeLoc("chrM", 1), rowData.split(" ")); TabularROD row = new TabularROD("myName", header, new GenomeLoc("chrM", 1), rowData.split(" "));
System.out.println(">>>>> " + row.toString());
assertTrue(row.toString().equals("chrM:1\t1\t2\t3")); assertTrue(row.toString().equals("chrM:1\t1\t2\t3"));
} }
@ -176,14 +177,14 @@ public class TabularRODTest extends BaseTest {
RODIterator iter_commas = ROD_commas.iterator(); RODIterator iter_commas = ROD_commas.iterator();
TabularROD one = (TabularROD)iter_commas.next(); TabularROD one = (TabularROD)iter_commas.next();
assertTrue(one.size() == 3); assertTrue(one.size() == 4);
assertTrue(one.getLocation().equals(new GenomeLoc("chrM", 1))); assertTrue(one.getLocation().equals(new GenomeLoc("chrM", 1)));
assertTrue(one.get("col1").equals("1")); assertTrue(one.get("col1").equals("1"));
assertTrue(one.get("col2").equals("2")); assertTrue(one.get("col2").equals("2"));
assertTrue(one.get("col3").equals("3")); assertTrue(one.get("col3").equals("3"));
TabularROD two = (TabularROD)iter_commas.next(); TabularROD two = (TabularROD)iter_commas.next();
assertTrue(two.size() == 3); assertTrue(two.size() == 4);
assertTrue(two.getLocation().equals(new GenomeLoc("chrM", 2))); assertTrue(two.getLocation().equals(new GenomeLoc("chrM", 2)));
assertTrue(two.get("col1").equals("3")); assertTrue(two.get("col1").equals("3"));
assertTrue(two.get("col2").equals("4")); assertTrue(two.get("col2").equals("4"));