bio.bam

Modules

abstractreader module bio.bam.abstractreader: Undocumented in source.
bai module bio.bam.bai
baifile module bio.bam.baifile: Undocumented in source.
baseinfo module bio.bam.baseinfo: Undocumented in source.
cigar module bio.bam.cigar: Undocumented in source.
constants module bio.bam.constants: Undocumented in source.
iontorrent module bio.bam.iontorrent
md module bio.bam.md
multireader module bio.bam.multireader: Undocumented in source.
pileup module bio.bam.pileup: This module is used for iterating over columns of alignment.
The function makePileup is called on a range of coordinate-sorted reads mapped to the same reference. It returns an input range of columns.
This returned range can then be iterated with foreach. First column is located at the same position on the reference, as the first base of the first read.
Each popFront operation advances current position on the reference. The default behaviour is to exclude sites with zero coverage from the iteration.
Each column keeps set of reads that overlap corresponding position on the reference. If reads contain MD tags, and makePileup was asked to use them, reference base at the column is also available.

Each read preserves all standard read properties but also keeps column-related information, namely <ul>
number of bases consumed from the read sequence so far
current CIGAR operation and offset in it
all CIGAR operations before and after current one
</ul>
It is clear from the above that current CIGAR operation cannot be an insertion. The following are suggested ways to check for them: <ul>
cigar_after.length > 0 && cigar_operation_offset == cigar_operation.length - 1 && cigar_after[0].type == 'I'
cigar_before.length > 0 && cigar_operation_offset == 0 && cigar_before[$ - 1].type == 'I'
</ul>
randomaccessmanager module bio.bam.randomaccessmanager: Module for random access operations on BAM file.
read module bio.bam.read: BamRead type provides convenient interface for working with SAM/BAM records.
reader module bio.bam.reader: Writing a script/tool for processing BAM data often starts this way:
readrange module bio.bam.readrange: Undocumented in source.
reference module bio.bam.reference: Each BAM file contains reads aligned to different reference sequences.
These sequences have unique identifiers in BAM file, starting from 0. Unmapped reads are associated with id = -1.
If BAI file is available, fast region queries are available, that is, getting all reads that overlap given region. This is achieved via opSlice method.
referenceinfo module bio.bam.referenceinfo: Undocumented in source.
region module bio.bam.region: Undocumented in source.
snpcallers module bio.bam.snpcallers
splitter module bio.bam.splitter: Undocumented in source.
tagvalue module bio.bam.tagvalue: BAM records may carry arbitrary information in tags.
Value type provides convenient way to work with this information.
thirdparty module bio.bam.thirdparty
utils module bio.bam.utils
validation module bio.bam.validation
writer module bio.bam.writer: Undocumented in source.

bio modules