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Updating AlignmentUtils.consolidateCigar() to the GATK coding standards.

This commit is contained in:
Ryan Poplin 2013-01-31 15:57:48 -05:00
parent b4db1d3e7f
commit e07cefb058
1 changed files with 3 additions and 2 deletions
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5
public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
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@ -508,12 +508,13 @@ public class AlignmentUtils {
* For example, 1M1M1M1D2M1M --> 3M1D3M * For example, 1M1M1M1D2M1M --> 3M1D3M
* If the given cigar is empty then the returned cigar will also be empty * If the given cigar is empty then the returned cigar will also be empty
* @param c the cigar to consolidate * @param c the cigar to consolidate
* @return a cigar with consecutive matching operators merged into single operators. * @return a non-null cigar with consecutive matching operators merged into single operators.
*/ */
@Requires({"c != null"})
@Ensures({"result != null"}) @Ensures({"result != null"})
public static Cigar consolidateCigar( final Cigar c ) { public static Cigar consolidateCigar( final Cigar c ) {
if( c == null ) { throw new IllegalArgumentException("Cigar cannot be null"); }
if( c.isEmpty() ) { return c; } if( c.isEmpty() ) { return c; }
final Cigar returnCigar = new Cigar(); final Cigar returnCigar = new Cigar();
int sumLength = 0; int sumLength = 0;
for( int iii = 0; iii < c.numCigarElements(); iii++ ) { for( int iii = 0; iii < c.numCigarElements(); iii++ ) {