Package | Description |
---|---|
htsjdk.samtools | |
htsjdk.samtools.cram | |
htsjdk.samtools.util |
Modifier and Type | Class and Description |
---|---|
class |
FileTruncatedException
Thrown when it is possible to detect that a SAM or BAM file is truncated.
|
class |
SAMFormatException
Thrown when a SAM file being read or decoded (text or binary) looks bad.
|
Modifier and Type | Method and Description |
---|---|
SAMRecord |
SAMRecordSetBuilder.addFrag(String name,
int contig,
int start,
boolean negativeStrand,
boolean recordUnmapped,
String cigar,
String qualityString,
int defaultQuality)
Adds a fragment record (mapped or unmapped) to the set using the provided contig start and optionally the strand,
cigar string, quality string or default quality score.
|
SAMRecord |
SAMRecordSetBuilder.addFrag(String name,
int contig,
int start,
boolean negativeStrand,
boolean recordUnmapped,
String cigar,
String qualityString,
int defaultQuality,
boolean isSecondary)
Adds a fragment record (mapped or unmapped) to the set using the provided contig start and optionally the strand,
cigar string, quality string or default quality score.
|
SAMRecord |
SAMRecordSetBuilder.addFrag(String name,
int contig,
int start,
boolean negativeStrand,
boolean recordUnmapped,
String cigar,
String qualityString,
int defaultQuality,
boolean isSecondary,
boolean isSupplementary)
Adds a fragment record (mapped or unmapped) to the set using the provided contig start and optionally the strand,
cigar string, quality string or default quality score.
|
Long |
SAMRecord.getUnsignedIntegerAttribute(short tag)
A convenience method that will return a valid unsigned integer as a Long,
or fail with an exception if the tag value is invalid.
|
Long |
SAMRecord.getUnsignedIntegerAttribute(String tag)
A convenience method that will return a valid unsigned integer as a Long,
or fail with an exception if the tag value is invalid.
|
Modifier and Type | Class and Description |
---|---|
class |
CRAMException
Created by edwardk on 8/13/15.
|
Modifier and Type | Class and Description |
---|---|
static class |
DateParser.InvalidDateException |
class |
RuntimeEOFException
Thrown by various codecs to indicate EOF without having to clutter the API with throws clauses
|
class |
RuntimeIOException
Thrown by various IO classes to indicate IOException without having to clutter the API with throws clauses
|
static class |
SequenceUtil.SequenceListsDifferException |