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Opens as BAM file if the specified filename ends in .bam. Otherwise it is opened as a SAM file.
Opens as BAM file if the specified filename ends in .bam. Otherwise it is opened as a SAM file.
Returns true if successfully opened for writing, false if not.
Returns true if successfully opened for writing, false if not.
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| void Close()
| Close the file if there is one open.
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| bool ReadHeader(SamFileHeader& header)
| bool ReadHeader(SamFileHeader& header)
| This method exists, but does not do anything and just returns false. This class is only for reading.
| This method exists, but does not do anything and just returns false. This class is only for reading.
Returns false.
Returns false.
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| void Close()
| Close the file if there is one open.
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| bool ReadHeader(SamFileHeader& header)
| bool ReadHeader(SamFileHeader& header)
Returns true if successfully set, false if not.
Returns true if successfully set, false if not.
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| bool setFlag(int flag)
| bool setFlag(int16_t flag)
| Sets the bitwise FLAG to the passed in value.
| Sets the bitwise FLAG to the passed in value.
Returns true if successfully set, false if not.
Returns true if successfully set, false if not.
Returns true if successfully set, false if not.
Returns true if successfully set, false if not.
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| bool set1BasedPosition(int position)
| bool set1BasedPosition(int32_t position)
| Sets the leftmost position. The value passed in is 1-based (SAM formatted). Internal processing handles switching between SAM/BAM formats when read/written.
| Sets the leftmost position. The value passed in is 1-based (SAM formatted). Internal processing handles switching between SAM/BAM formats when read/written.
Returns true if successfully set, false if not.
Returns true if successfully set, false if not.
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| bool set0BasedPosition(int position)
| bool set0BasedPosition(int32_t position)
| Sets the leftmost position. The value passed in is 0-based (BAM formatted). Internal processing handles switching between SAM/BAM formats when read/written.
| Sets the leftmost position. The value passed in is 0-based (BAM formatted). Internal processing handles switching between SAM/BAM formats when read/written.
Returns true if successfully set, false if not.
Returns true if successfully set, false if not.
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|bool setMapQuality(int mapQuality)
|bool setMapQuality(int8_t mapQuality)
| Sets the mapping quality.
| Sets the mapping quality.
Returns true if successfully set, false if not.
Returns true if successfully set, false if not.
Returns true if successfully set, false if not.
Returns true if successfully set, false if not.
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| bool set1BasedMatePosition(int matePosition)
| bool set1BasedMatePosition(int32_t matePosition)
| Sets the leftmost mate position. The value passed in is 1-based (SAM formatted). Internal processing handles switching between SAM/BAM formats when read/written.
| Sets the leftmost mate position. The value passed in is 1-based (SAM formatted). Internal processing handles switching between SAM/BAM formats when read/written.
Returns true if successfully set, false if not.
Returns true if successfully set, false if not.
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| bool set0BasedMatePosition(int matePosition)
| bool set0BasedMatePosition(int32_t matePosition)
| Sets the leftmost mate position. The value passed in is 0-based (BAM formatted). Internal processing handles switching between SAM/BAM formats when read/written.
| Sets the leftmost mate position. The value passed in is 0-based (BAM formatted). Internal processing handles switching between SAM/BAM formats when read/written.
Returns true if successfully set, false if not.
Returns true if successfully set, false if not.
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| bool setInsertSize(int insertSize)
| bool setInsertSize(int32_t insertSize)
| Sets the inferred insert size.
| Sets the inferred insert size.
Returns true if successfully set, false if not.
Returns true if successfully set, false if not.
| Returns true if the record is valid. This performs validation steps. TODO: the method exists, but it does not yet perform any checks, so just returns true.
| Returns true if the record is valid. This performs validation steps. TODO: the method exists, but it does not yet perform any checks, so just returns true.
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| int getBlockSize()
| int32_t getBlockSize()
| Returns the BAM block size of the record.
| Returns the BAM block size of the record.
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| const char* getReferenceName()
| const char* getReferenceName(SamFileHeader& header)
| Returns the reference sequence name (SAM format).
| Returns the reference sequence name (SAM format).
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| int getReferenceID()
| int32_t getReferenceID()
| Returns the reference sequence ID (BAM format).
| Returns the reference sequence ID (BAM format).
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| int get1BasedPosition()
| int32_t get1BasedPosition()
| Returns the 1-based (SAM formatted) leftmost position.
| Returns the 1-based (SAM formatted) leftmost position.
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| int get0BasedPosition()
| int32_t get0BasedPosition()
| Returns the 0-based (BAM formatted) leftmost position.
| Returns the 0-based (BAM formatted) leftmost position.
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| int getReadNameLength()
| int8_t getReadNameLength()
| Returns the length of the ReadName (QNAME).
| Returns the length of the ReadName (QNAME).
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| int getMapQuality()
| int8_t getMapQuality()
| Returns the map quality.
| Returns the map quality.
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| int getBin()
| int16_t getBin()
| Returns the BAM bin for the record.
| Returns the BAM bin for the record.
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| int getCigarLength()
| int16_t getCigarLength()
| Returns the length of the CIGAR in BAM format.
| Returns the length of the CIGAR in BAM format.
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| int getFlag()
| int16_t getFlag()
| Returns the flag.
| Returns the flag.
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| int getReadLength()
| int32_t getReadLength()
| Returns the length of the read.
| Returns the length of the read.
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| const char* getMateReferenceName()
| const char* getMateReferenceName(SamFileHeader& header)
| Returns the mate reference sequence name (SAM format). Returns the mate reference sequence name even if it is the same as the reference sequence name.
| Returns the mate reference sequence name (SAM format). Returns the mate reference sequence name even if it is the same as the reference sequence name.
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| const char* getMateReferenceNameOrEqual()
| const char* getMateReferenceNameOrEqual(SamFileHeader& header)
| Returns the mate reference sequence name (SAM format). Returns the mate reference sequence name, unless it is the same as the reference sequence name, then an "=" is returned..
| Returns the mate reference sequence name (SAM format). Returns the mate reference sequence name, unless it is the same as the reference sequence name, then an "=" is returned..
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| int getMateReferenceID()
| int32_t getMateReferenceID()
| Returns the mate reference sequence id (BAM format).
| Returns the mate reference sequence id (BAM format).
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| int get1BasedMatePosition()
| int32_t get1BasedMatePosition()
| Returns the 1-based (SAM formatted) mate leftmost position.
| Returns the 1-based (SAM formatted) mate leftmost position.
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| int get0BasedMatePosition()
| int32_t get0BasedMatePosition()
| Returns the 0-based (BAM formatted) mate leftmost position.
| Returns the 0-based (BAM formatted) mate leftmost position.
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| int getInsertSize()
| int32_t getInsertSize()
| Returns the insert size.
| Returns the insert size.
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| int32_t get0BasedAlignmentEnd();
| Returns the 0-based inclusive right-most position of the clipped sequence.
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| int32_t get1BasedAlignmentEnd();
| Returns the 1-based inclusive right-most position of the clipped sequence.
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| int32_t get0BasedUnclippedStart();
| Returns the 0-based inclusive left-most position adjusted for clipped bases.
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| int32_t get1BasedUnclippedStart();
| Returns the 1-based inclusive left-most position adjusted for clipped bases.
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| int32_t get0BasedUnclippedEnd();
| Returns the 0-based inclusive right-most position adjusted for clipped bases.
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| int32_t get1BasedUnclippedEnd();
| Returns the 1-based inclusive right-most position adjusted for clipped bases.
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| const char* getReadName()
| const char* getReadName()
