Many resources are needed to download a project. Please understand that we have to compensate our server costs. Thank you in advance. Project price only 1 $
You can buy this project and download/modify it how often you want.
package htsjdk.samtools;
import htsjdk.samtools.util.Log;
import java.io.File;
import java.util.Collections;
import java.util.Optional;
import java.util.SortedMap;
import java.util.TreeMap;
/**
* Embodies defaults for global values that affect how the SAM JDK operates. Defaults are encoded in the class
* and are also overridable using system properties.
*
* @author Tim Fennell
*/
public class Defaults {
private static final Log log = Log.getInstance(Defaults.class);
/** Should BAM index files be created when writing out coordinate sorted BAM files? Default = false. */
public static final boolean CREATE_INDEX;
/** Should MD5 files be created when writing out SAM and BAM files? Default = false. */
public static final boolean CREATE_MD5;
/** Should asynchronous read I/O be used where supported by the samtools package (one thread per file).
* Default = false.
*/
public static final boolean USE_ASYNC_IO_READ_FOR_SAMTOOLS;
/** Should asynchronous write I/O be used where supported by the samtools package (one thread per file).
* Default = false.
*/
public static final boolean USE_ASYNC_IO_WRITE_FOR_SAMTOOLS;
/** Should asynchronous write I/O be used where supported by the tribble package (one thread per file).
* Default = false.
*/
public static final boolean USE_ASYNC_IO_WRITE_FOR_TRIBBLE;
/** Compression level to be used for writing BAM and other block-compressed outputs. Default = 5. */
public static final int COMPRESSION_LEVEL;
/** Buffer size, in bytes, used whenever reading/writing files or streams. Default = 128k. */
public static final int BUFFER_SIZE;
/** The output format of the flag field when writing SAM text. Ignored for reading SAM text. Default = DECIMAL */
public static final SamFlagField SAM_FLAG_FIELD_FORMAT;
/**
* The extension to assume a sam file has when the actual file doesn't have an extension, useful
* for when outputing to /dev/stdout, for example.
*/
public static final String DEFAULT_SAM_EXTENSION;
/**
* The extension to assume a vcf has when the actual file doesn't have an extension, useful
* for when outputing to /dev/stdout, for example.
*/
public static final String DEFAULT_VCF_EXTENSION;
/**
* Even if BUFFER_SIZE is 0, this is guaranteed to be non-zero. If BUFFER_SIZE is non-zero,
* this == BUFFER_SIZE (Default = 128k).
*/
public static final int NON_ZERO_BUFFER_SIZE;
/**
* The reference FASTA file. If this is not set, the file is null. This file may be required for reading
* writing SAM files (ex. CRAM). Default = null.
*/
public static final File REFERENCE_FASTA;
/** Custom reader factory able to handle URL based resources like ga4gh.
* Expected format: ,[,]
* E.g. https://www.googleapis.com/genomics/v1beta/reads/,com.google.genomics.ReaderFactory
* OR https://www.googleapis.com/genomics/v1beta/reads/,com.google.genomics.ReaderFactory,/tmp/genomics.jar
* Default = "".
*/
public static final String CUSTOM_READER_FACTORY;
/**
* Boolean describing whether downloading a reference file is allowed (for CRAM files),
* in case the reference file is not specified by the user
* Enabling this is not necessarily a good idea, since this process often fails. Default = false.
*/
public static final boolean USE_CRAM_REF_DOWNLOAD;
/**
* A mask (pattern) to use when building EBI reference service URL for a
* given MD5 checksum. Must contain one and only one string placeholder.
* Default = "https://www.ebi.ac.uk/ena/cram/md5/%s".
*/
public static final String EBI_REFERENCE_SERVICE_URL_MASK;
/**
* Boolean describing whether downloading of SRA native libraries is allowed,
* in case such native libraries are not found locally. Default = false.
*/
public static final boolean SRA_LIBRARIES_DOWNLOAD;
/**
* The name of the system property that disables snappy. Default = "snappy.disable".
*/
public static final String DISABLE_SNAPPY_PROPERTY_NAME = "snappy.disable";
/**
* Disable use of the Snappy compressor. Default = false.
*/
public static final boolean DISABLE_SNAPPY_COMPRESSOR;
public static final String SAMJDK_PREFIX = "samjdk.";
static {
CREATE_INDEX = getBooleanProperty("create_index", false);
CREATE_MD5 = getBooleanProperty("create_md5", false);
USE_ASYNC_IO_READ_FOR_SAMTOOLS = getBooleanProperty("use_async_io_read_samtools", false);
USE_ASYNC_IO_WRITE_FOR_SAMTOOLS = getBooleanProperty("use_async_io_write_samtools", false);
USE_ASYNC_IO_WRITE_FOR_TRIBBLE = getBooleanProperty("use_async_io_write_tribble", false);
COMPRESSION_LEVEL = getIntProperty("compression_level", 5);
DEFAULT_SAM_EXTENSION = getStringProperty("default_sam_type", "bam");
DEFAULT_VCF_EXTENSION = getStringProperty("default_vcf_type", "vcf");
BUFFER_SIZE = getIntProperty("buffer_size", 1024 * 128);
if (BUFFER_SIZE == 0) {
NON_ZERO_BUFFER_SIZE = 1024 * 128;
} else {
NON_ZERO_BUFFER_SIZE = BUFFER_SIZE;
}
REFERENCE_FASTA = getFileProperty("reference_fasta", null);
USE_CRAM_REF_DOWNLOAD = getBooleanProperty("use_cram_ref_download", false);
EBI_REFERENCE_SERVICE_URL_MASK = "https://www.ebi.ac.uk/ena/cram/md5/%s";
CUSTOM_READER_FACTORY = getStringProperty("custom_reader", "");
SAM_FLAG_FIELD_FORMAT = SamFlagField.valueOf(getStringProperty("sam_flag_field_format", SamFlagField.DECIMAL.name()));
SRA_LIBRARIES_DOWNLOAD = getBooleanProperty("sra_libraries_download", false);
DISABLE_SNAPPY_COMPRESSOR = getBooleanProperty(DISABLE_SNAPPY_PROPERTY_NAME, false);
}
/**
* Returns a map of all default values (keys are names), lexicographically sorted by keys.
* The returned map is unmodifiable.
* This function is useful for example when logging all defaults.
*/
public static SortedMap allDefaults(){
final SortedMap result = new TreeMap<>();
result.put("CREATE_INDEX", CREATE_INDEX);
result.put("CREATE_MD5", CREATE_MD5);
result.put("USE_ASYNC_IO_READ_FOR_SAMTOOLS", USE_ASYNC_IO_READ_FOR_SAMTOOLS);
result.put("USE_ASYNC_IO_WRITE_FOR_SAMTOOLS", USE_ASYNC_IO_WRITE_FOR_SAMTOOLS);
result.put("USE_ASYNC_IO_WRITE_FOR_TRIBBLE", USE_ASYNC_IO_WRITE_FOR_TRIBBLE);
result.put("COMPRESSION_LEVEL", COMPRESSION_LEVEL);
result.put("BUFFER_SIZE", BUFFER_SIZE);
result.put("NON_ZERO_BUFFER_SIZE", NON_ZERO_BUFFER_SIZE);
result.put("REFERENCE_FASTA", REFERENCE_FASTA);
result.put("USE_CRAM_REF_DOWNLOAD", USE_CRAM_REF_DOWNLOAD);
result.put("EBI_REFERENCE_SERVICE_URL_MASK", EBI_REFERENCE_SERVICE_URL_MASK);
result.put("CUSTOM_READER_FACTORY", CUSTOM_READER_FACTORY);
result.put("SAM_FLAG_FIELD_FORMAT", SAM_FLAG_FIELD_FORMAT);
result.put("DISABLE_SNAPPY_COMPRESSOR", DISABLE_SNAPPY_COMPRESSOR);
return Collections.unmodifiableSortedMap(result);
}
/** Gets a string system property, prefixed with "samjdk." using the default
* if the property does not exist or if the java.security manager raises an exception for
* applications started with -Djava.security.manager . */
private static String getStringProperty(final String name, final String def) {
try {
return System.getProperty(Defaults.SAMJDK_PREFIX + name, def);
} catch (final java.security.AccessControlException error) {
log.warn(error,"java Security Manager forbids 'System.getProperty(\"" + name + "\")' , returning default value: " + def );
return def;
}
}
/** Checks whether a string system property, prefixed with "samjdk.", exists.
* If the property does not exist or if the java.security manager raises an exception for
* applications started with -Djava.security.manager this method returns false. */
private static boolean hasProperty(final String name){
try {
return null != System.getProperty(Defaults.SAMJDK_PREFIX + name);
} catch (final java.security.AccessControlException error) {
log.warn(error,"java Security Manager forbids 'System.getProperty(\"" + name + "\")' , returning false");
return false;
}
}
/** Gets a boolean system property, prefixed with "samjdk." using the default if the property does not exist. */
private static boolean getBooleanProperty(final String name, final boolean def) {
final String value = getStringProperty(name, Boolean.toString(def));
return Boolean.parseBoolean(value);
}
/** Gets an int system property, prefixed with "samjdk." using the default if the property does not exist. */
private static int getIntProperty(final String name, final int def) {
final String value = getStringProperty(name, Integer.toString(def));
return Integer.parseInt(value);
}
/** Gets a File system property, prefixed with "samjdk." using the default if the property does not exist. */
private static File getFileProperty(final String name, final String def) {
final String value = getStringProperty(name, def);
Optional maybeFile = Optional.ofNullable(value).map(File::new);
maybeFile.ifPresent(f -> {
if (!f.exists()) {
log.warn(String.format("File property for %s has value %s. However file %s doesn't exist.", SAMJDK_PREFIX + name, value, f.getAbsolutePath()));
} else {
log.info(String.format("Found file for property %s: %s ", SAMJDK_PREFIX + name, f.getAbsolutePath()));
}
});
return maybeFile.orElse(null);
}
}
