Converts a single ADAM record into a SAM record.
Converts a single ADAM record into a SAM record.
ADAM formatted alignment to convert.
SAM file header to attach to the record.
Dictionary describing the read groups that are in the RDD that this read is from.
Returns the record converted to htsjdk format. Can be used for output to SAM/BAM.
Converts a fragment to a set of reads.
Converts a fragment to a set of reads.
Fragment to convert.
The collection of alignments described by the fragment. If the fragment doesn't contain any alignments, this method will return one unaligned Alignment per sequence in the Fragment.
Converts a single record representing the second read of a pair to Bowtie tab5 format.
Converts a single record representing the second read of a pair to Bowtie tab5 format.
In Bowtie tab5 format, each alignment or pair is on a single line. An unpaired alignment line is [name]\t[seq]\t[qualityScores]\n. A paired-end read line is [name]\t[seq1]\t[qualityScores1]\t[seq2]\t[qualityScores2]\n.
If the base quality scores are unknown (qualityScores is null or equals "*"), the quality scores will be a repeated string of 'B's that is equal to the read length.
Read to convert to FASTQ.
If true and the original base quality scores field is set (SAM "OQ" tag), outputs the original quality scores. Else, output the qualityScores field. Defaults to false.
Returns this read in string form.
Converts a single record to FASTQ format.
Converts a single record to FASTQ format.
FASTQ format is:
@readName sequence +<optional readname> ASCII quality scores
If the base quality scores are unknown (qualityScores is null or equals "*"), the quality scores will be a repeated string of 'B's that is equal to the read length.
Read to convert to FASTQ.
If true, check if a "/%d" suffix is attached to the read. If there is no suffix, a slash and the number of the read in the sequenced fragment is appended to the readname. Default is false.
If true and the original base quality score field is set (SAM "OQ" tag), outputs the original quality scores. Else, output the qualityScores field. Defaults to false.
Returns this read in string form.
Converts a single record to Bowtie tab5 format.
Converts a single record to Bowtie tab5 format.
In Bowtie tab5 format, each alignment or pair is on a single line. An unpaired alignment line is [name]\t[seq]\t[qualityScores]\n. A paired-end read line is [name]\t[seq1]\t[qualityScores1]\t[seq2]\t[qualityScores2]\n.
The index suffix will be trimmed from the read name if present.
If the base quality scores are unknown (qualityScores is null or equals "*"), the quality scores will be a repeated string of 'B's that is equal to the read length.
Read to convert to FASTQ.
If true and the original base quality scores field is set (SAM "OQ" tag), outputs the original quality scores. Else, output the qualityScores field. Defaults to false.
Returns this read in string form.
Converts a single record to Bowtie tab6 format.
Converts a single record to Bowtie tab6 format.
In Bowtie tab6 format, each alignment or pair is on a single line. An unpaired alignment line is [name]\t[seq]\t[qualityScores]\n. For paired-end alignments, the second end can have a different name from the first: [name1]\t[seq1]\t[qualityScores1]\t[name2]\t[seq2]\t[qualityScores2]\n.
If the base quality scores are unknown (qualityScores is null or equals "*"), the quality scores will be a repeated string of 'B's that is equal to the read length.
Read to convert to FASTQ.
If true, check if a "/%d" suffix is attached to the read. If there is no suffix, a slash and the number of the read in the sequenced fragment is appended to the readname. Default is false.
If true and the original base quality scores field is set (SAM "OQ" tag), outputs the original quality scores. Else, output the qualityScores field. Defaults to false.
Returns this read in string form.
Creates a SAM formatted header.
Creates a SAM formatted header. This can be used with SAM or BAM files.
Reference sequence dictionary to use for conversion.
Dictionary containing read groups.
Converted SAM formatted record.
This class contains methods to convert Alignments to other formats.