org.broadinstitute.hellbender.utils.test

Class SamAssertionUtils

java.lang.Object

org.broadinstitute.hellbender.utils.test.SamAssertionUtils

public final class SamAssertionUtils
extends java.lang.Object

Collection of utilities for making common assertions about SAM files for unit testing purposes.

Constructor Summary

Constructors

Constructor and Description
SamAssertionUtils()

Method Summary

Modifier and Type	Method and Description
static void	assertCRAMContents(java.nio.file.Path putativeCRAMPath) Unconditionally validate/assert that the contents are CRAM
static void	assertCRAMContentsIfCRAM(java.io.File putativeCRAMFile) Validate/assert that the contents are CRAM if the extension is .cram
static void	assertCRAMContentsIfCRAM(java.nio.file.Path putativeCRAMPath) Validate/assert that the contents are CRAM if the extension is .cram
static void	assertEqualBamFiles(java.io.File resultFile, java.io.File expectedFile, boolean compareBamFilesSorted, htsjdk.samtools.ValidationStringency stringency) Compares the two given bam files, optionally sorting them before comparison.
static void	assertEqualBamFiles(java.io.File resultFile, java.io.File expectedFile, java.io.File reference, boolean compareBamFilesSorted, htsjdk.samtools.ValidationStringency stringency) Compares the two given bam files, optionally sorting them before comparison.
static void	assertSamsEqual(java.io.File actualSam, java.io.File expectedSam) causes an exception if the given sam files aren't equal
static void	assertSamsEqual(java.io.File actualSam, java.io.File expectedSam, java.io.File reference) causes an exception if the given sam files aren't equal
static void	assertSamsEqual(java.io.File actualSam, java.io.File expectedSam, htsjdk.samtools.ValidationStringency validationStringency) causes an exception if the given sam files aren't equal
static void	assertSamsEqual(java.io.File actualSam, java.io.File expectedSam, htsjdk.samtools.ValidationStringency validationStringency, java.io.File reference) causes an exception if the given sam files aren't equal
static void	assertSamsEqual(java.nio.file.Path actualSam, java.nio.file.Path expectedSam, java.nio.file.Path reference)
static void	assertSamsEqual(java.nio.file.Path actualSam, java.nio.file.Path expectedSam, htsjdk.samtools.ValidationStringency validationStringency, java.nio.file.Path reference)
static void	assertSamValid(java.io.File sam) causes an exception if the given sam isn't valid the default ValidationStringency value for this method is LENIENT
static void	assertSamValid(java.io.File sam, java.io.File reference) causes an exception if the given sam isn't valid
static void	assertSamValid(java.io.File sam, htsjdk.samtools.ValidationStringency validationStringency) causes an exception if the given sam isn't valid
static void	assertSamValid(java.io.File sam, htsjdk.samtools.ValidationStringency validationStringency, java.io.File reference) causes an exception if the given sam isn't valid
static java.lang.String	samsEqualLenient(java.io.File actualSam, java.io.File expectedSam, htsjdk.samtools.ValidationStringency validation, java.io.File reference) Compares SAM/BAM files in a stringent way but not by byte identity (allow reorder of attributes).
static java.lang.String	samsEqualStringent(java.io.File actualSam, java.io.File expectedSam, htsjdk.samtools.ValidationStringency validation, java.io.File reference) Compares SAM/BAM files in a stringent way but not by byte identity (allow reorder of attributes) Comparing by MD5s is too strict and comparing by SamComparison is too lenient.
static java.lang.String	samsEqualStringent(java.nio.file.Path actualSam, java.nio.file.Path expectedSam, htsjdk.samtools.ValidationStringency validation, java.nio.file.Path reference) Compares SAM/BAM files in a stringent way but not by byte identity (allow reorder of attributes) Comparing by MD5s is too strict and comparing by SamComparison is too lenient.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SamAssertionUtils

public SamAssertionUtils()

Method Detail

assertSamsEqual

public static void assertSamsEqual(java.io.File actualSam,
                                   java.io.File expectedSam,
                                   htsjdk.samtools.ValidationStringency validationStringency,
                                   java.io.File reference)
                            throws java.io.IOException

causes an exception if the given sam files aren't equal

Parameters:

actualSam - the actual file

expectedSam - the expected file

validationStringency - how stringently do we validate the files

reference - is allowed to be null

Throws:

java.io.IOException

assertSamsEqual

public static void assertSamsEqual(java.nio.file.Path actualSam,
                                   java.nio.file.Path expectedSam,
                                   htsjdk.samtools.ValidationStringency validationStringency,
                                   java.nio.file.Path reference)
                            throws java.io.IOException

Throws:

java.io.IOException

assertSamsEqual

public static void assertSamsEqual(java.io.File actualSam,
                                   java.io.File expectedSam,
                                   htsjdk.samtools.ValidationStringency validationStringency)
                            throws java.io.IOException

causes an exception if the given sam files aren't equal

Parameters:

actualSam - the actual file

expectedSam - the expected file

validationStringency - how stringently do we validate the files

Throws:

java.io.IOException

assertSamsEqual

public static void assertSamsEqual(java.io.File actualSam,
                                   java.io.File expectedSam,
                                   java.io.File reference)
                            throws java.io.IOException

causes an exception if the given sam files aren't equal

Parameters:

actualSam - the actual file

expectedSam - the expected file

reference - is allowed to be null

Throws:

java.io.IOException

assertSamsEqual

public static void assertSamsEqual(java.nio.file.Path actualSam,
                                   java.nio.file.Path expectedSam,
                                   java.nio.file.Path reference)
                            throws java.io.IOException

Throws:

java.io.IOException

assertSamsEqual

public static void assertSamsEqual(java.io.File actualSam,
                                   java.io.File expectedSam)
                            throws java.io.IOException

causes an exception if the given sam files aren't equal

Parameters:

actualSam - the actual file

expectedSam - the expected file

Throws:

java.io.IOException

assertSamValid

public static void assertSamValid(java.io.File sam,
                                  htsjdk.samtools.ValidationStringency validationStringency,
                                  java.io.File reference)
                           throws java.io.IOException

causes an exception if the given sam isn't valid

Parameters:

reference - is allowed to be null

Throws:

java.io.IOException

assertSamValid

public static void assertSamValid(java.io.File sam,
                                  htsjdk.samtools.ValidationStringency validationStringency)
                           throws java.io.IOException

causes an exception if the given sam isn't valid

Throws:

java.io.IOException

assertSamValid

public static void assertSamValid(java.io.File sam,
                                  java.io.File reference)
                           throws java.io.IOException

causes an exception if the given sam isn't valid

Parameters:

reference - is allowed to be null the default ValidationStringency value for this method is LENIENT

Throws:

java.io.IOException

assertSamValid

public static void assertSamValid(java.io.File sam)
                           throws java.io.IOException

causes an exception if the given sam isn't valid the default ValidationStringency value for this method is LENIENT

Throws:

java.io.IOException

samsEqualLenient

public static java.lang.String samsEqualLenient(java.io.File actualSam,
                                                java.io.File expectedSam,
                                                htsjdk.samtools.ValidationStringency validation,
                                                java.io.File reference)
                                         throws java.io.IOException

Compares SAM/BAM files in a stringent way but not by byte identity (allow reorder of attributes). Returns null if the files are considered equals and returns a String describing the reason for comparison failure. The lenient comparison only checks headers and alignment info SamComparison. Compares headers, and if headers are compatible enough, compares SAMRecords, looking only at basic alignment info.

Throws:

java.io.IOException

samsEqualStringent

public static java.lang.String samsEqualStringent(java.io.File actualSam,
                                                  java.io.File expectedSam,
                                                  htsjdk.samtools.ValidationStringency validation,
                                                  java.io.File reference)
                                           throws java.io.IOException

Compares SAM/BAM files in a stringent way but not by byte identity (allow reorder of attributes) Comparing by MD5s is too strict and comparing by SamComparison is too lenient. So we need this method. This differs from a byte-to-byte comparison: - @PG and @CO lines in headers are ignored in the comparison. - each read in the actual file are allowed to have a superset of the attributes of the corresponding read in the expected set

Returns:

null if equal or message string if not equal.

Throws:

java.io.IOException

samsEqualStringent

public static java.lang.String samsEqualStringent(java.nio.file.Path actualSam,
                                                  java.nio.file.Path expectedSam,
                                                  htsjdk.samtools.ValidationStringency validation,
                                                  java.nio.file.Path reference)
                                           throws java.io.IOException

Compares SAM/BAM files in a stringent way but not by byte identity (allow reorder of attributes) Comparing by MD5s is too strict and comparing by SamComparison is too lenient. So we need this method. This differs from a byte-to-byte comparison: - @PG and @CO lines in headers are ignored in the comparison. - each read in the actual file are allowed to have a superset of the attributes of the corresponding read in the expected set

Returns:

null if equal or message string if not equal.

Throws:

java.io.IOException

assertEqualBamFiles

public static void assertEqualBamFiles(java.io.File resultFile,
                                       java.io.File expectedFile,
                                       boolean compareBamFilesSorted,
                                       htsjdk.samtools.ValidationStringency stringency)
                                throws java.io.IOException

Compares the two given bam files, optionally sorting them before comparison. The sorting is helpful to compare files that are different but equivalent (eg read pairs with same coordinates get reordered).

Throws:

java.io.IOException

assertEqualBamFiles

public static void assertEqualBamFiles(java.io.File resultFile,
                                       java.io.File expectedFile,
                                       java.io.File reference,
                                       boolean compareBamFilesSorted,
                                       htsjdk.samtools.ValidationStringency stringency)
                                throws java.io.IOException

Compares the two given bam files, optionally sorting them before comparison. The sorting is helpful to compare files that are different but equivalent (eg read pairs with same coordinates get reordered).

Throws:

java.io.IOException

assertCRAMContentsIfCRAM

public static void assertCRAMContentsIfCRAM(java.io.File putativeCRAMFile)

Validate/assert that the contents are CRAM if the extension is .cram

assertCRAMContentsIfCRAM

public static void assertCRAMContentsIfCRAM(java.nio.file.Path putativeCRAMPath)

Validate/assert that the contents are CRAM if the extension is .cram

assertCRAMContents

public static void assertCRAMContents(java.nio.file.Path putativeCRAMPath)

Unconditionally validate/assert that the contents are CRAM