bamreader v0.2.1

BAMReader

BAMReader is a reader to parse .bam files. Uses samtools If exists, otherwise uses a native parser.

installation

$ npm install -g bamreader

usage

var BAMReader = require("bamreader");
var reader = BAMReader.create("/path/to/bamfile.bam");
reader.on("bam", function(bam) {
  // bam: object. see "bam object" section
  console.log(bam.seq, bam.qual);
  console.log(bam.pair); // pair bam object of the bam. To do this, indexing is needed.
});

reader.on("end", function() {
  console.log("all bam alignments have been read.");
});

bam object

• pair : information of the mate pair. see "bam.pair"
• discordant : discordant or not. see "bam.discordant"
• qname : name of the read
• flag : bitwise flag
• rname : reference sequence rname
• pos : 1-based leftmost mapping position
• mapq : mapping quality
• cigar : CIGAR string
• rnext : reference sequence name of the primary alignment of the next read
• next_rname : the actual reference name of the next read.
• pnext : position of the primary alignment of the next read
• tlen : template length
• seq : segment jsequence
• qual : ASCII of base quality plus 33
• start : 0-based leftmost mapping position
• flags : information of flags
• tagstr : optional fields as string
• tags : optional fields as structured data described in "bamdata.tags" section
• multiple : information from flag: template have multiple segment or not.
• unmapped : information from flag: unmapped or not.
• allmatches : information from flag: each segment properly aligned or not
• next_unmapped : information from flag: next segment is unmapped or not.
• reversed : information from flag: reversely mapped or not.
• next_reversed : information from flag: next segment is reversely mapped or not.
• first : information from flag: first segment or not.
• last : information from flag: last segment or not.
• secondary : information from flag: secondary alignment or not.
• lowquality : information from flag: not passing quality control or not.
• duplicate : information from flag: PCR or optic duplicate or not.
• supplementary : information from flag: supplementary alignment or not.
• clipped : clipped or not.
• soft_clipped : soft-clipped or not.
• hard_clipped : hard-clipped or not.
• left_break : the left position of the breakpoint if clipped.
• right_break : the right position of the breakpoint if clipped.
• match_len : length of the matched portion of the read.
• fully_matched : if the whole base of the read is matched or not
• mismatch : the number of mismatch bases
• unique : if the read is mapped uniquely or not
• indel : the mapping result contains insertion/deletion or not.
• different_ref : if both mapped and rname is not rnext or not
• same_strand : if both mapped and mapped to the same strand or not
• has_n : the read contains "N" or not
• sam : SAM formatted string of the bam

bam.pair

bamreader can fetch one mate pair of the read using index.

$ bamreader -c <bamfile>     # creates an index of the bamfile.

then you can access bam.pair

bam.pair is also a bam object.

bam.discordant

(...)

bam.tags

• (key): tag name (two string character)
• (value): type: data type, value: data

if data type is "B", value0 is subtype, value.slice(1) is the array of data.