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LICENSE

Copyright [2015-2018] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

NAME

Bio::DB::HTS -- Read files using HTSlib including BAM/CRAM, Tabix and BCF database files

SYNOPSIS

 use Bio::DB::HTS;

 # high level API
 # Note that the high level API does not reset the CRAM file pointer to the start
 # of the file as the method to do so is (at time or writing) not easily accessible.
 # Therefore a new HTS object may be needed to repeat a query.
 my $hts = Bio::DB::HTS->new(-bam  =>"data/ex1.bam",
                             -fasta=>"data/ex1.fa",
                             );

 my @targets    = $hts->seq_ids;
 my @alignments = $hts->get_features_by_location(-seq_id => 'seq2',
                                                 -start  => 500,
                                                 -end    => 800);
 for my $a (@alignments) {

    # where does the alignment start in the reference sequence
    my $seqid  = $a->seq_id;
    my $start  = $a->start;
    my $end    = $a->end;
    my $strand = $a->strand;
    my $cigar  = $a->cigar_str;
    my $paired = $a->get_tag_values('PAIRED');

    # where does the alignment start in the query sequence
    my $query_start = $a->query->start;
    my $query_end   = $a->query->end;

    my $ref_dna   = $a->dna;        # reference sequence bases
    my $query_dna = $a->query->dna; # query sequence bases

    my @scores    = $a->qscore;     # per-base quality scores
    my $match_qual= $a->qual;       # quality of the match
 }

 my @pairs = $hts->get_features_by_location(-type   => 'read_pair',
                                            -seq_id => 'seq2',
                                            -start  => 500,
                                            -end    => 800);

 for my $pair (@pairs)
 {
    my $length                    = $pair->length;   # insert length
    my ($first_mate,$second_mate) = $pair->get_SeqFeatures;
    my $f_start = $first_mate->start;
    my $s_start = $second_mate->start;
 }

 # low level API
 my $hfile        = Bio::DB::HTSfile->open('/path/to/alignment_file');
 my $header       = $hfile->header_read;
 my $target_count = $header->n_targets;
 my $target_names = $header->target_name;
 while (my $align = $hfile->read1($header))
 {
    my $seqid     = $target_names->[$align->tid];
    my $start     = $align->pos+1;
    my $end       = $align->calend;
    my $cigar     = $align->cigar_str;
 }

 Bio::DB::HTSfile->index_build($bamfile);
 my $index = Bio::DB::HTSfile->index_load($hfile);
 my $index = Bio::DB::HTSfile->index_open_in_safewd($hfile);

 my $callback = sub {
     my $alignment = shift;
     my $start       = $alignment->start;
     my $end         = $alignment->end;
     my $seqid       = $target_names->[$alignment->tid];
     print $alignment->qname," aligns to $seqid:$start..$end\n";
 }
 my $header = $index->header;
 $index->fetch($hfile,$header->parse_region('seq2'),$callback);

DESCRIPTION

This module provides a Perl interface to the HTSlib library for indexed and unindexed SAM/BAM/CRAM sequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information across large regions. It also provides callback functionality for calling SNPs and performing other base-by-base functions.

The high-level API

The high-level API provides a BioPerl-compatible interface to indexed BAM and CRAM files. The alignment file database is treated as a collection of Bio::SeqFeatureI features, and can be searched for features by name, location, type and combinations of feature tags such as whether the alignment is part of a mate-pair.

When opening a alignment database using the high-level API, you provide the pathnames of two files: the FASTA file that contains the reference genome sequence, and the BAM file that contains the query sequences and their alignments. If either of the two files needs to be indexed, the indexing will need to be built. You can then query the database for alignment features by combinations of name, position, type, and feature tag.

The high-level API provides access to up to four feature "types":

 * "match": The "raw" unpaired alignment between a read and the
   reference sequence.

 * "read_pair": Paired alignments; a single composite
   feature that contains two subfeatures for the alignments of each
   of the mates in a mate pair.

 * "coverage": A feature that spans a region of interest that contains
   numeric information on the coverage of reads across the region.

 * "region": A way of retrieving information about the reference
   sequence. Searching for features of type "region" will return a
   list of chromosomes or contigs in the reference sequence, rather
   than read alignments.

 * "chromosome": A synonym for "region".

Features can be en masse in a single call, retrieved in a memory-efficient streaming basis using an iterator, or interrogated using a filehandle that return a series of SAM-format lines.

SAM alignment flags can be retrieved using BioPerl's feature "tag" mechanism. For example, to interrogate the FIRST_MATE flag, one fetches the "FIRST_MATE" tag:

  warn "aye aye captain!" if $alignment->get_tag_values('FIRST_MATE');

The Bio::SeqFeatureI interface has been extended to retrieve all flags as a compact human-readable string, and to return the CIGAR alignment in a variety of formats.

Split alignments, such as reads that cover introns, are dealt with in one of two ways. The default is to leave split alignments alone: they can be detected by one or more "N" operations in the CIGAR string. Optionally, you can choose to have the API split these alignments across two or more subfeatures; the CIGAR strings of these split alignments will be adjusted accordingly.

Interface to the pileup routines The API provides you with access to the samtools "pileup" API. This gives you the ability to write a callback that will be invoked on every column of the alignment for the purpose of calculating coverage, quality score metrics, or SNP calling.

Access to the reference sequence When you create the Bio::DB::HTS object, you can pass the path to a FASTA file containing the reference sequence. Alternatively, you may pass an object that knows how to retrieve DNA sequences across a range via the seq() or fetch_seq() methods, as described under new().

If the SAM/BAM file has MD tags, then these tags will be used to reconstruct the reference sequence when necessary, in which case you can completely omit the -fasta argument. Note that not all SAM/BAM files have MD tags, and those that do may not use them correctly due to the newness of this part of the SAM spec. You may wish to populate these tags using samtools' "calmd" command.

If the -fasta argument is omitted and no MD tags are present, then the reference sequence will be returned as 'N'.

The main object classes that you will be dealing with in the high-level API are as follows:

 * Bio::DB::HTS               -- A collection of alignments and reference sequences.
 * Bio::DB::HTS::Alignment    -- The alignment between a query and the reference.
 * Bio::DB::HTS::Query        -- An object corresponding to the query sequence in
                                  which both (+) and (-) strand alignments are
                                  shown in the reference (+) strand.
 * Bio::DB::HTS::Target       -- An interface to the query sequence in which
                                   (-) strand alignments are shown in reverse
                                   complement

You may encounter other classes as well. These include:

 * Bio::DB::HTS::Segment       -- This corresponds to a region on the reference
                                  sequence.
 * Bio::DB::HTS::Constants     -- This defines CIGAR symbol constants and flags.
 * Bio::DB::HTS::AlignWrapper  -- An alignment helper object that adds split
                                  alignment functionality. See Bio::DB::HTS::Alignment
                                  for the documentation on using it.
 * Bio::DB::HTS::ReadIterator  -- An iterator that mediates the one-feature-at-a-time
                                  retrieval mechanism.
 * Bio::DB::HTS::FetchIterator -- Another iterator for feature-at-a-time retrieval.

The low-level API

The low-level API closely mirrors that of the HTSlib library. It provides the ability to open and read SAM, BAM and CRAM files, build indexes, and perform searches across them.

The classes you will be interacting with in the low-level API are as follows:

 * Bio::DB::HTS            -- Methods that read and write SAM, BAM and CRAM files.
 * Bio::DB::HTS::Header    -- Methods for manipulating the BAM file header.
 * Bio::DB::HTS::Alignment -- Methods for manipulating alignment data.
 * Bio::DB::HTS::Pileup    -- Methods for manipulating the pileup data structure.
 * Bio::DB::HTS::Fai       -- Methods for creating and reading from indexed Fasta
                              files.

METHODS

We cover the high-level API first. The high-level API code can be found in the files Bio/DB/HTS.pm and Bio/DB/HTS/*.pm.

Bio::DB::HTS Constructor and basic accessors

$sam = Bio::DB::HTS->new(%options)

The Bio::DB::HTS object combines a Fasta file of the reference sequences with an SAM/BAM/CRAM alignment file to allow for convenient retrieval of human-readable sequence IDs and reference sequences. The new() constructor accepts a -name=>value style list of options as follows:

  Option         Description
  ------         -------------

  -bam           Path to the SAM/BAM/CRAM alignment file that contains the
                 alignments (required). A http: or ftp: URL is accepted.

  -fasta         Path to the Fasta file that contains
                 the reference sequences (optional). Alternatively,
                 you may pass any object that supports a seq()
                 or fetch_seq() method and takes the three arguments
                 ($seq_id,$start,$end).

  -expand_flags  A boolean value. If true then the standard
                 alignment flags will be broken out as
                 individual tags such as 'M_UNMAPPED' (default false).

  -split_splices A boolean value. If true, then alignments that
                 are split across splices will be broken out
                 into a single alignment containing two sub-
                 alignments (default false).

  -split         The same as -split_splices.

  -force_refseq  Always use the reference sequence file to derive the
                 reference sequence, even when the sequence can be
                 derived from the MD tag. This is slower, but safer
                 when working with BAM files derived from buggy aligners
                 or when the reference contains non-canonical (modified)
                 bases.

  -autoindex     Create an alignment index file if one does not exist
                 or the current one has a modification date
                 earlier than the alignment file.

An example of a typical new() constructor invocation is:

  $hts = Bio::DB::HTS->new(-fasta => '/home/projects/genomes/hu17.fa',
                           -bam   => '/home/projects/alignments/ej88.bam',
                           -expand_flags  => 1,
                           -split_splices => 1);

If the -fasta argument is present, then you will be able to use the interface to fetch the reference sequence's bases. Otherwise, calls that return the reference sequence will return sequences consisting entirely of "N".

-expand_flags option, if true, has the effect of turning each of the standard SAM flags into a separately retrievable tag in the Bio::SeqFeatureI interface. Otherwise, the standard flags will be concatenated in easily parseable form as a tag named "FLAGS". See get_all_tags() and get_tag_values() for more information.

Any two-letter extension flags, such as H0 or H1, will always appear as separate tags regardless of the setting.

-split_splices has the effect of breaking up alignments that contain an "N" operation into subparts for more convenient manipulation. For example, if you have both paired reads and spliced alignments in the BAM file, the following code shows the subpart relationships:

  $pair        = $hts->get_feature_by_name('E113:01:01:23');
  @mates       = $pair->get_SeqFeatures;
  @mate1_parts = $mates[0]->get_SeqFeatures;
  @mate2_parts = $mates[1]->get_SeqFeatures;

Because there is some overhead to splitting up the spliced alignments, this option is false by default.

Remote access to alignment files located on an HTTP or FTP server is possible. Simply replace the path to the BAM file with the appropriate URL. Note that incorrect URLs may lead to a core dump.

It is not currently possible to refer to a remote FASTA file. These will have to be downloaded locally and indexed before using.

$flag = $hts->expand_flags([$new_value])

Get or set the expand_flags option. This can be done after object creation and will have an immediate effect on all alignments fetched from the alignment file.

$flag = $hts->split_splices([$new_value])

Get or set the split_splices option. This can be done after object creation and will affect all alignments fetched from the alignment file subsequently.

$header = $hts->header

Return the Bio::DB::HTS::Header object associated with the alignment file. You can manipulate the header using the low-level API.

$hts_path = $hts->hts_path

Return the path of the alignment file used to create the hts object. This makes the object more portable.

$hts_file = $hts->$hts_file

Returns the low-level Bio::DB::HTSfile object associated with the opened file.

$fai = $hts->fai

Returns the Bio::DB::HTS::Fai object associated with the Fasta file. You can then manipulate this object with the low-level API.

The index can be built automatically for you if it does not already exist. If index building is necessarily, the process will need write privileges to the same directory in which the Fasta file resides.> If the process does not have write permission, then the call will fail.

$hts_idx = $hts->hts_index

Return the Bio::DB::HTS::Index object associated with the alignment file.

The index is not automatically built.

$hts->clone

Bio::DB::HTS objects are not stable across fork() operations. If you fork, you must call clone() either in the parent or the child process before attempting to call any methods.

Getting information about reference sequences

The Bio::DB::HTS object provides the following methods for getting information about the reference sequence(s) contained in the associated Fasta file.

@seq_ids = $hts->seq_ids

Returns an unsorted list of the IDs of the reference sequences (known elsewhere in this document as seq_ids). This is the same as the identifier following the ">" sign in the Fasta file (e.g. "chr1").

$num_targets = $hts->n_targets

Return the number of reference sequences.

$length = $hts->length('seqid')

Returns the length of the reference sequence named "seqid".

$seq_id = $hts->target_name($tid)

Translates a numeric target ID (TID) returned by the low-level API into a seq_id used by the high-level API.

$length = $hts->target_len($tid)

Translates a numeric target ID (TID) from the low-level API to a sequence length.

$dna = $hts->seq($seqid,$start,$end)

Returns the DNA across the region from start to end on reference seqid. Note that this is a string, not a Bio::PrimarySeq object. If no -fasta path was passed when the sam object was created, then you will receive a series of N nucleotides of the requested length.

Creating and querying segments

Bio::DB::HTS::Segment objects refer regions on the reference sequence. They can be used to retrieve the sequence of the reference, as well as alignments that overlap with the region.

$segment = $hts->segment($seqid,$start,$end);
$segment = $hts->segment(-seq_id=>'chr1',-start=>5000,-end=>6000);

Segments are created using the Bio:DB::HTS->segment() method. It can be called using one to three positional arguments corresponding to the seq_id of the reference sequence, and optionally the start and end positions of a subregion on the sequence. If the start and/or end are undefined, they will be replaced with the beginning and end of the sequence respectively.

Alternatively, you may call segment() with named -seq_id, -start and -end arguments.

All coordinates are 1-based.

$seqid = $segment->seq_id

Return the segment's sequence ID.

$start = $segment->start

Return the segment's start position.

$end = $segment->end

Return the segment's end position.

$strand = $segment->strand

Return the strand of the segment (always 0).

$length = $segment->length

Return the length of the segment.

$dna = $segment->dna

Return the DNA string for the reference sequence under this segment.

$seq = $segment->seq

Return a Bio::PrimarySeq object corresponding to the sequence of the reference under this segment. You can get the actual DNA string in this redundant-looking way:

 $dna = $segment->seq->seq

The advantage of working with a Bio::PrimarySeq object is that you can perform operations on it, including taking its reverse complement and subsequences.

@alignments = $segment->features(%args)

Return alignments that overlap the segment in the associated alignment file. The optional %args list allows you to filter features by name, tag or other attributes. See the documentation of the Bio::DB::HTS->features() method for the full list of options. Here are some typical examples:

 # get all the overlapping alignments
 @all_alignments = $segment->features;

 # get an iterator across the alignments
 my $iterator     = $segment->features(-iterator=>1);
 while (my $align = $iterator->next_seq) { do something }

 # get a SAM filehandle across the alignments
 my $fh           = $segment->features(-fh=>1);
 while (<$fh>) { print }

 # get only the alignments with unmapped mates
 my @unmapped    = $segment->features(-flags=>{M_UNMAPPED=>1});

 # get coverage across this region
 my ($coverage)       = $segment->features('coverage');
 my @data_points      = $coverage->coverage;

 # grep through features using a coderef
 my @reverse_alignments = $segment->features(
                           -filter => sub {
                                  my $a = shift;
                                  return $a->strand < 0;
                               });
$tag = $segment->primary_tag
$tag = $segment->source_tag

Return the strings "region" and "sam/bam" respectively. These methods allow the segment to be passed to BioPerl methods that expect Bio::SeqFeatureI objects.

$segment->name, $segment->display_name, $segment->get_SeqFeatures, $segment->get_tag_values

These methods are provided for Bio::SeqFeatureI compatibility and don't do anything of interest.

Retrieving alignments, mate pairs and coverage information

The features() method is an all-purpose tool for retrieving alignment information from the SAM/BAM/CRAM alignment file database. In addition, the methods get_features_by_name(), get_features_by_location() and others provide convenient shortcuts to features().

These methods either return a list of features, an iterator across a list of features, or a filehandle opened on a pseudo-SAM file.

@features = $hts->features(%options)
$iterator = $hts->features(-iterator=>1,%more_options)
$filehandle = $hts->features(-fh=>1,%more_options)
@features = $hts->features('type1','type2'...)

This is the all-purpose interface for fetching alignments and other types of features from the database. Arguments are a -name=>value option list selected from the following list of options:

  Option         Description
  ------         -------------

  -type          Filter on features of a given type. You may provide
                 either a scalar typename, or a reference to an
                 array of desired feature types. Valid types are
                 "match", "read_pair", "coverage" and "chromosome."

                 See below for a full explanation of feature types.

  -name          Filter on reads with the designated name. Note that
                 this can be a slow operation unless accompanied by
                 the feature location as well.

  -seq_id        Filter on features that align to seq_id between start
  -start         and end. -start and -end must be used in conjunction
  -end           with -seq_id. If -start and/or -end are absent, they
                 will default to 1 and the end of the reference
                 sequence, respectively.

  -flags         Filter features that match a list of one or more
                 flags. See below for the format.

  -attributes    The same as -flags, for compatibility with other
  -tags          APIs.

  -filter        Filter on features with a coderef. The coderef will
                 receive a single argument consisting of the feature
                 and should return true to keep the feature, or false
                 to discard it.

  -iterator      Instead of returning a list of features, return an
                 iterator across the results. To retrieve the results,
                 call the iterator's next_seq() method repeatedly
                 until it returns undef to indicate that no more
                 matching features remain.

  -fh            Instead of returning a list of features, return a
                 filehandle. Read from the filehandle to retrieve
                 each of the results in TAM format, one alignment
                 per line read. This only works for features of type
                 "match."

The high-level API introduces the concept of a feature "type" in order to provide several convenience functions. You specify types by using the optional -type argument. The following types are currently supported:

match. The "match" type corresponds to the unprocessed SAM alignment. It will retrieve single reads, either mapped or unmapped. Each match feature's primary_tag() method will return the string "match." The features returned by this call are of type Bio::DB::HTS::AlignWrapper.

read_pair. The "paired_end" type causes the sam interface to find and merge together mate pairs. Fetching this type of feature will yield a series of Bio::SeqFeatureI objects, each as long as the total distance on the reference sequence spanned by the mate pairs. The top-level feature is of type Bio::SeqFeature::Lite; it contains two Bio::DB::HTS::AlignWrapper subparts.

Call get_SeqFeatures() to get the two individual reads. Example:

 my @pairs    = $hts->features(-type=>'read_pair');
 my $p        = $pairs[0];
 my $i_length = $p->length;
 my @ends     = $p->get_SeqFeatures;
 my $left     = $ends[0]->start;
 my $right    = $ends[1]->end;

coverage. The "coverage" type causes the sam interface to calculate coverage across the designated region. It only works properly if accompanied by the desired location of the coverage graph; -seq_id is a mandatory argument for coverage calculation, and -start and -end are optional. The call will return a single Bio::SeqFeatureI object whose primary_tag() is "coverage." To recover the coverage data, call the object's coverage() method to obtain an array (list context) or arrayref (scalar context) of coverage counts across the region of interest:

 my ($coverage) = $hts->features(-type=>'coverage',-seq_id=>'seq1');
 my @data       = $coverage->coverage;
 my $total;
 for (@data) { $total += $_ }
 my $average_coverage = $total/@data;

By default the coverage graph will be at the base pair level. So for a region 5000 bp wide, coverage() will return an array or arrayref with exactly 5000 elements. However, you also have the option of calculating the coverage across larger bins. Simply append the number of intervals you are interested to the "coverage" typename. For example, fetching "coverage:500" will return a feature whose coverage() method will return the coverage across 500 intervals.

chromosome or region. The "chromosome" or "region" type are interchangeable. They ask the sam interface to construct Bio::DB::HTS::Segment representing the reference sequences. These two calls give similar results:

 my $segment = $hts->segment('seq2',1=>500);
 my ($seg)   = $hts->features(-type=>'chromosome',
                              -seq_id=>'seq2',-start=>1,-end=>500);

Due to an unresolved bug, you cannot fetch chromosome features in the same call with matches and other feature types call. Specifically, this works as expected:

 my @chromosomes = $hts->features (-type=>'chromosome');

But this doesn't (as of 18 June 2009):

 my @chromosomes_and_matches = $hts->features(-type=>['match','chromosome']);

If no -type argument is provided, then features() defaults to finding features of type "match."

You may call features() with a plain list of strings (positional arguments, not -type=>value arguments). This will be interpreted as a list of feature types to return:

 my ($coverage) = $hts->features('coverage')

For a description of the methods available in the features returned from this call, please see Bio::SeqfeatureI and Bio::DB::HTS::Alignment.

You can filter "match" and "read_pair" features by name, location and/or flags. The name and flag filters are not very efficient. Unless they are combined with a location filter, they will initiate an exhaustive search of the BAM database.

Name filters are case-insensitive, and allow you to use shell-style "*" and "?" wildcards. Flag filters created with the -flag, -attribute or -tag options have the following syntax:

 -flag => { FLAG_NAME_1 => ['list','of','possible','values'],
            FLAG_NAME_2 => ['list','of','possible','values'],
            ...
          }

The value of -flag is a hash reference in which the keys are flag names and the values are array references containing lists of acceptable values. The list of values are OR'd with each other, and the flag names are AND'd with each other.

The -filter option provides a completely generic filtering interface. Provide a reference to a subroutine. It will be called once for each potential feature. Return true to keep the feature, or false to discard it. Here is an example of how to find all matches whose alignment quality scores are greater than 80.

 @features = $hts->features(-filter=>sub {shift->qual > 80} );

By default, features() returns a list of all matching features. You may instead request an iterator across the results list by passing -iterator=>1. This will give you an object that has a single method, next_seq():

  my $high_qual  = $hts->features(-filter  => sub {shift->qual > 80},
                                  -iterator=> 1 );
  while (my $feature = $high_qual->next_seq) {
    # do something with the alignment
  }

Similarly, by passing a true value to the argument -fh, you can obtain a filehandle to a virtual SAM file. This only works with the "match" feature type:

  my $high_qual  = $hts->features(-filter  => sub {shift->qual > 80},
                                  -fh      => 1 );
  while (my $tam_line = <$high_qual>) {
    chomp($tam_line);
    # do something with it
  }
@features = $hts->get_features_by_name($name)

Convenience method. The same as calling $hts->features(-name=>$name);

$feature = $hts->get_feature_by_name($name)

Convenience method. The same as ($hts->features(-name=>$name))[0].

@features = $hts->get_features_by_location($seqid,$start,$end)

Convenience method. The same as calling $hts->features(-seq_id=>$seqid,-start=>$start,-end=>$end).

@features = $hts->get_features_by_flag(%flags)

Convenience method. The same as calling $hts->features(-flags=>\%flags). This method is also called get_features_by_attribute() and get_features_by_tag(). Example:

 @features = $hts->get_features_by_flag(H0=>1)
$feature = $hts->get_feature_by_id($id)

The high-level API assigns each feature a unique ID composed of its read name, position and strand and returns it when you call the feature's primary_id() method. Given that ID, this method returns the feature.

$iterator = $hts->get_seq_stream(%options)

Convenience method. This is the same as calling $hts->features(%options,-iterator=>1).

$fh = $hts->get_seq_fh(%options)

Convenience method. This is the same as calling $hts->features(%options,-fh=>1).

$fh = $hts->tam_fh

Convenience method. It is the same as calling $hts->features(-fh=>1).

@types = $hts->types

This method returns the list of feature types (e.g. "read_pair") returned by the current version of the interface.

The generic fetch() and pileup() methods

Lastly, the high-level API supports two methods for rapidly traversing indexed BAM databases.

$hts->fetch($region,$callback)

This method traverses the indicated region and invokes a callback code reference on each match. Specify a region using the syntax "seqid:start-end", or either of the alternative syntaxes "seqid:start..end" and "seqid:start,end". If start and end are absent, then the entire reference sequence is traversed. If end is absent, then the end of the reference sequence is assumed.

The callback will be called repeatedly with a Bio::DB::HTS::AlignWrapper on the argument list.

Example:

  $hts->fetch('seq1:600-700',
              sub {
                my $a = shift;
                print $a->display_name,' ',$a->cigar_str,"\n";
              });

Note that the fetch() operation works on reads that overlap the indicated region. Therefore the callback may be called for reads that align to the reference at positions that start before or end after the indicated region.

$hts->pileup($region,$callback [,$keep_level])

This method, which is named after the native bam_lpileupfile() function in the C interfaces, traverses the indicated region and generates a "pileup" of all the mapped reads that cover it. The user-provided callback function is then invoked on each position of the alignment along with a data structure that provides access to the individual aligned reads.

As with fetch(), the region is specified as a string in the format "seqid:start-end", "seqid:start..end" or "seqid:start,end".

The callback is a coderef that will be invoked with three arguments: the seq_id of the reference sequence, the current position on the reference (in 1-based coordinates!), and a reference to an array of Bio::DB::HTS::Pileup objects. Here is the typical call signature:

  sub {
       my ($seqid,$pos,$pileup) = @_;
       # do something
  }

For example, if you call pileup on the region "seq1:501-600", then the callback will be invoked for all reads that overlap the indicated region. The first invocation of the callback will typically have a $pos argument somewhat to the left of the desired region and the last call will be somewhat to the right. You may wish to ignore positions that are outside of the requested region. Also be aware that the reference sequence position uses 1-based coordinates, which is different from the low-level interface, which use 0-based coordinates.

The size of the $pileup array reference indicates the read coverage at that position. Here is a simple average coverage calculator:

 my $depth      = 0;
 my $positions  = 0;
 my $callback = sub {
         my ($seqid,$pos,$pileup) = @_;
         next unless $pos >= 501 && $pos <= 600;
         $positions++;
         $depth += @$pileup;
 }
 $hts->pileup('seq1:501-600',$callback);
 print "coverage = ",$depth/$positions;

Each Bio::DB::HTS::Pileup object describes the position of a read in the alignment. Briefly, Bio::DB::HTS::Pileup has the following methods:

 $pileup->alignment  The alignment at this level (a
                     Bio::DB::HTS::AlignWrapper object).

 $pileup->qpos   The position of the read base at the pileup site,
                 in 0-based coordinates.

 $pileup->pos    The position of the read base at the pileup site,
                 in 1-based coordinates;

 $pileup->level  The level of the read in the multiple alignment
                 view. Note that this field is only valid when
                 $keep_level is true, so it may not be relevant post
                 htslib move.

 $pileup->indel  Length of the indel at this position: 0 for no indel, positive
                 for an insertion (relative to the reference), negative for a
                 deletion (relative to the reference.)

 $pileup->is_del True if the base on the padded read is a deletion.

 $pileup->is_refskip True if the base on the padded read is a gap relative to the reference (denoted as < or > in the pileup)

 $pileup->is_head True if this is the first base in the query sequence.

 $pileup->is_tail True if this is the last base in the query sequence.

See "Examples" for a very simple SNP caller.

$hts->fast_pileup($region,$callback [,$keep_level])

This is identical to pileup() except that the pileup object returns low-level Bio::DB::HTS::Alignment objects rather than the higher-level Bio::DB::HTS::AlignWrapper objects. This makes it roughly 50% faster, but you lose the align objects' seq_id() and get_tag_values() methods. As a compensation, the callback receives an additional argument corresponding to the Bio::DB::HTS object. You can use this to create AlignWrapper objects on an as needed basis:

 my $callback = sub {
    my($seqid,$pos,$pileup,$hts) = @_;
    for my $p (@$pileup) {
       my $alignment = $p->alignment;
       my $wrapper   = Bio::DB::HTS::AlignWrapper->new($alignment,$hts);
       my $has_mate  = $wrapper->get_tag_values('PAIRED');
    }
  };
Bio::DB::HTS->max_pileup_cnt([$new_cnt])
$hts->max_pileup_cnt([$new_cnt])

The HTSlib library caps pileups at a set level, defaulting to 8000. The callback will not be invoked on a single position more than the level set by the cap, even if there are more reads. Called with no arguments, this method returns the current cap value. Called with a numeric argument, it changes the cap. There is currently no way to specify an unlimited cap.

This method can be called as an instance method or a class method.

$hts->coverage2BedGraph([$fh])

This special-purpose method will compute a four-column BED graph of the coverage across the entire alignment file and print it to STDOUT. You may provide a filehandle to redirect output to a file or pipe.

The next sections correspond to the low-level API, which let you create and manipulate Perl objects that correspond directly to data structures in the C interface. A major difference between the high and low level APIs is that in the high-level API, the reference sequence is identified using a human-readable seq_id. However, in the low-level API, the reference is identified using a numeric target ID ("tid"). The target ID is established during the creation of the alignment file and is a small 0-based integer index. The Bio::DB::HTS::Header object provides methods for converting from seq_ids to tids.

Indexed Fasta Files

These methods relate to the indexed Fasta (".fai") files.

$fai = Bio::DB::HTS::Fai->load('/path/to/file.fa')

Load an indexed Fasta file and return the object corresponding to it. If the index does not exist, it will be created automatically. Note that you pass the path to the Fasta file, not the index.

For consistency with Bio::DB::HTS->open() this method is also called open().

$dna_string = $fai->fetch("seqid:start-end")

Given a sequence ID contained in the Fasta file and optionally a subrange in the form "start-end", finds the indicated subsequence and returns it as a string.

Alignment Files

These methods provide interfaces to alignment files in SAM/BAM/CRAM format.

$hts_file = Bio::DB::HTSfile->open('/path/to/file.bam' [,$mode])

Open the alignment file at the indicated path. Mode, if present, must be one of the file stream open flags ("r", "w", "wb", "wc", "a", "r+", etc.). If absent, mode defaults to "r". [write formats: w = SAM, wb = BAM, wc = CRAM]

Note that Bio::DB::HTS objects are not stable across fork() operations. If you fork, and intend to use the object in both parent and child, you must reopen the Bio::DB::HTS in either the child or the parent (but not both) before attempting to call any of the object's methods.

The path may be an http: or ftp: URL, in which case a copy of the index file will be downloaded to the current working directory (see below) and all accesses will be performed on the remote BAM file.

Example:

   $hfile = Bio::DB::HTSfile->open('http://some.site.com/nextgen/chr1_bowtie.bam');
$header = $hfile->header_read()

Given an open alignment file, return a Bio::DB::HTS::Header object containing information about the reference sequence(s). Note that you must invoke header_read() at least once before calling read1().

$status_code = $hfile->header_write($header, [$reference])

Given a Bio::DB::HTSfile::Header object and a BAM file opened in write mode, write the header to the file. If the write fails the process will be terminated at the C layer. If $hfile is CRAM formated a second argument $reference, which is the path to the reference Fasta file, must be passed. The result code is (currently) always zero.

$alignment = $hfile->read1($header)

Read one alignment from the alignment file and return it as a Bio::DB::HTS::Alignment object. The $header parameter is returned by invoking header().

$bytes = $hfile->write1($header, $alignment)

Given a BAM file that has been opened in write mode and a Bio::DB::HTS::Alignment object, write the alignment to the BAM file and return the number of bytes successfully written.

Index methods

The Bio::DB::HTS::Index object provides access to index (.bai|.csi, .crai) files.

$status_code = Bio::DB::HTS->index_build('/path/to/file.?am')

Given the path to an alignment file, this function attempts to build an index. The process in which the alignment file exists must be writable by the current process and there must be sufficient disk space for the operation or the process will be terminated in the C library layer. The result code is currently always zero, but in the future may return a negative value to indicate failure.

The index file built will depend on the alignment file type specified. For CRAM this will be a .crai file, for BAM .bai.

$index = Bio::DB::HTS->index('/path/to/file.?am',$reindex)

Attempt to open the index for the indicated alignment file. If $reindex is true, and the index either does not exist or is out of date with respect to the alignment file (by checking modification dates), then attempt to rebuild the index. Will throw an exception if the index does not exist or if attempting to rebuild the index was unsuccessful.

$index = Bio::DB::HTS->index_load('/path/to/file.?am')

Attempt to open the index file for an alignment file, returning a Bio::DB::HTS::Index object. The filename path to use is the alignment file, not the index file (i.e. .bam or .cram, not .bai|.csi or .crai)

$index = Bio::DB::HTS->index_open_in_safewd('/path/to/file.?am' [,$mode])

When opening a remote alignmentfile, you may not wish for the index to be downloaded to the current working directory. This version of index_open copies the index into the directory indicated by the TMPDIR environment variable or the system-defined /tmp directory if not present. You may change the environment variable just before the call to change its behavior.

$code = $index->fetch($hfile,$tid,$start,$end,$callback [,$callback_data])

This is the low-level equivalent of the $hts->fetch() function described for the high-level API. Given a open BAM file object, the numeric ID of the reference sequence, start and end ranges on the reference, and a coderef, this function will traverse the region and repeatedly invoke the coderef with each Bio::DB::HTS::Alignment object that overlaps the region.

Arguments:

 Argument      Description
 --------      -----------

 $hts_file     The Bio::DB::HTSfile object that corresponds to the
               index object.

 $tid          The target ID of the reference sequence. This can
               be obtained by calling $header->parse_region() with
               an appropriate opened Bio::DB::HTS::Header object.

 $start        The start and end positions of the desired range on
               the reference sequence given by $tid, in 0-based
 $end          coordinates. Like the $tid, these can be obtained from
               $header->parse_region().

 $callback     A coderef that will be called for each read overlapping
               the designated region.

 $callback_data  Any arbitrary Perl data that you wish to pass to the
               $callback (optional).

The coderef's call signature should look like this:

  my $callback = sub {
                    my ($alignment,$data) = @_;
                    ...
                 }

The first argument is a Bio::DB::HTS::Alignment object. The second is the callback data (if any) passed to fetch().

Fetch() returns an integer code, but its meaning is not described in the SAM/BAM C library documentation.

$index->pileup($htsfile,$tid,$start,$end,$callback [,$callback_data])

This is the low-level version of the pileup() method, which allows you to invoke a coderef for every position in a BAM alignment. Arguments are:

 Argument      Description
 --------      -----------

 $hts_file     The Bio::DB::HTSfile object that corresponds to the
               index object.

 $tid          The target ID of the reference sequence. This can
               be obtained by calling $header->parse_region() with
               an appropriate opened Bio::DB::HTS::Header object.

 $start        The start and end positions of the desired range on
               the reference sequence given by $tid, in 0-based
 $end          coordinates. Like the $tid, these can be obtained from
               $header->parse_region().

 $callback     A coderef that will be called for each position of the
               alignment across the designated region.

 $callback_data  Any arbitrary Perl data that you wish to pass to the
                 $callback (optional).

The callback will be invoked with four arguments corresponding to the numeric sequence ID of the reference sequence, the zero-based position on the alignment, an arrayref of Bio::DB::HTS::Pileup objects, and the callback data, if any. A typical call signature will be this:

 $callback = sub {
       my ($tid,$pos,$pileups,$callback_data) = @_;
       for my $pileup (@$pileups) {
          # do something
       };

Note that the position argument is zero-based rather than 1-based, as it is in the high-level API.

The Bio::DB::HTS::Pileup object was described earlier in the description of the high-level pileup() method.

$coverage = $index->coverage($hfile,$tid,$start,$end [,$bins [,maxcnt]])

Calculate coverage for the region on the target sequence given by $tid between positions $start and $end (zero-based coordinates). This method will return an array reference equal to the size of the region (by default). Each element of the array will be an integer indicating the number of reads aligning over that position. If you provide an option binsize in $bins, the array will be $bins elements in length, and each element will contain the average coverage over that region as a floating point number.

By default, the underlying Samtools library caps coverage counting at a fixed value of 8000. You may change this default by providing an optional numeric sixth value, which changes the cap for the duration of the call, or by invoking Bio::DB::HTS->max_pileup_cnt($new_value), which changes the cap permanently. Unfortunately there is no way of specifying that you want an unlimited cap.

HTS header methods

The Bio::DB::HTS::Header object contains information regarding the reference sequence(s) used to construct the corresponding alignment file. It is most frequently used to translate between numeric target IDs and human-readable seq_ids. Headers can be created by reading from a BAM file using Bio::DB::HTS->header(). You can also create header objects from scratch, although there is not much that you can do with such objects at this point.

$header = Bio::DB::HTS::Header->new()

Return a new, empty, header object.

$n_targets = $header->n_targets

Return the number of reference sequences in the database.

$name_arrayref = $header->target_name

Return a reference to an array of reference sequence names, corresponding to the high-level API's seq_ids.

To convert from a target ID to a seq_id, simply index into this array:

 $seq_id = $header->target_name->[$tid];
$length_arrayref = $header->target_len

Return a reference to an array of reference sequence lengths. To get the length of the sequence corresponding to $tid, just index into the array returned by target_len():

 $length = $header->target_len->[$tid];
$text = $header->text
$header->text("new value")

Read the text portion of the header. The text can be replaced by providing the replacement string as an argument. Note that you should follow the header conventions when replacing the header text. No parsing or other error-checking is performed.

($tid,$start,$end) = $header->parse_region("seq_id:start-end")

Given a string in the format "seqid:start-end" (using a human-readable seq_id and 1-based start and end coordinates), parse the string and return the target ID and start and end positions in 0-based coordinates. If the range is omitted, then the start and end coordinates of the entire sequence is returned. If only the end position is omitted, then the end of the sequence is assumed.

$header->view1($alignment)

This method will accept a Bio::DB::HTS::Alignment object, convert it to a line of TAM output, and write the output to STDOUT. In the low-level API there is currently no way to send the output to a different filehandle or capture it as a string.

Bio::DB::HTS::Pileup methods

An array of Bio::DB::HTS::Pileup object is passed to the pileup() callback for each position of a multi-read alignment. Each pileup object contains information about the alignment of a single read at a single position.

$alignment = $pileup->alignment

Return the Bio::DB::HTS::Alignment object at this level. This provides you with access to the aligning read.

$alignment = $pileup->b

An alias for alignment(), provided for compatibility with the C API.

$pos = $pileup->qpos

The position of the aligning base in the read in zero-based coordinates.

$pos = $pileup->pos

The position of the aligning base in 1-based coordinates.

$level = $pileup->level

The "level" of the read in the BAM-generated text display of the alignment.

$indel = $pileup->indel

Length of the indel at this position: 0 for no indel, positive for an insertion (relative to the reference), negative for a deletion (relative to the reference sequence.)

$flag = $pileup->is_del

True if the base on the padded read is a deletion.

$flag = $pileup->is_refskip

True if the base on the padded read is a gap relative to the reference (denoted as < or > in the pileup)

$flag = $pileup->is_head

True if this is the first base in the query sequence.

$flag = $pileup->is_tail

True if this is the last base in the query sequence.

The alignment objects

Please see Bio::DB::HTS::Alignment for documentation of the Bio::DB::HTS::Alignment and Bio::DB::HTS::AlignWrapper objects.

DEPENDENCIES

Module::Build, Carp, Bio::Perl (>=1.006001), Test::More

EXPORT

None

AUTHORS

Rishi Nag <rishi@ebi.ac.uk>, original author.

Alessandro Vullo <avullo at cpan.org>, the current developer and maintainer.

CONTRIBUTORS

Andy Yates, Keiran Raine, John Marshall, Zhicheng Liu, Can Wood, Dietmar Rieder, Chris Fields, David Jones, James Gilbert, Alex Hodgkins (Congenica Ltd.), Rob Aganrab

KNOWN BUGS

  • SAM file reading and iterating over alignments does not work with older htslib versions (<1.5)

  • The padded_alignment() function with CRAM files may produce invalid output: unequal lenght of the strings that specify the pairwise alignment

Please report any bugs or feature requests to bug-bio-db-hts at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-DB-HTS. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

TESTING AND CONTRIBUTING

You can obtain the most recent development version of this module via the GitHub repository at https://github.com/Ensembl/Bio-DB-HTS. Please feel free to submit bug reports, patches etc.

SUPPORT

You can find documentation for this module with the perldoc command.

    perldoc Bio::DB::HTS

You can also look for information at:

EXAMPLES

For illustrative purposes only, here is an extremely stupid SNP caller that tallies up bases that are q>20 and calls a SNP if there are at least 4 non-N/non-indel bases at the position and at least 25% of them are a non-reference base.

 my @SNPs;  # this will be list of SNPs
 my $snp_caller = sub {
        my ($seqid,$pos,$p) = @_;
        my $refbase = $hts->segment($seqid,$pos,$pos)->dna;
        my ($total,$different);
        for my $pileup (@$p) {
            my $b     = $pileup->alignment;
            next if $pileup->indel or $pileup->is_refskip;      # don't deal with these ;-)

            my $qbase  = substr($b->qseq,$pileup->qpos,1);
            next if $qbase =~ /[nN]/;

            my $qscore = $b->qscore->[$pileup->qpos];
            next unless $qscore > 25;

            $total++;
            $different++ if $refbase ne $qbase;
        }
        if ($total >= 4 && $different/$total >= 0.25) {
           push @SNPs,"$seqid:$pos";
        }
    };

 $hts->pileup('seq1',$snp_caller);
 print "Found SNPs: @SNPs\n";

GBrowse Compatibility

The Bio::DB::HTS interface can be used as a backend to GBrowse (gmod.sourceforge.net/gbrowse). GBrowse can calculate and display coverage graphs across large regions, alignment cartoons across intermediate size regions, and detailed base-pair level alignments across small regions.

Here is a typical configuration for a BAM database that contains information from a shotgun genomic sequencing project. Some notes:

 * It is important to set "search options = none" in order to avoid
   GBrowse trying to scan through the BAM database to match read
   names. This is a time-consuming operation.

 * The callback to "bgcolor" renders pairs whose mates are unmapped in
   red.

 * The callback to "balloon hover" causes a balloon to pop up with the
   read name when the user hovers over each paired read. Otherwise the
   default behavior would be to provide information about the pair as
   a whole.

 * When the user zooms out to 1001 bp or greaterp, the track switches
   to a coverage graph.

 [bamtest:database]
 db_adaptor    = Bio::DB::HTSfile
 db_args       = -bam   /var/www/gbrowse2/databases/bamtest/ex1.bam
 search options= default

 [Pair]
 feature       = read_pair
 glyph         = segments
 database      = bamtest
 draw_target   = 1
 show_mismatch = 1
 bgcolor      = sub {
                 my $f = shift;
                 return $f->get_tag_values('M_UNMAPPED') ? 'red' : 'green';
               }
 fgcolor       = green
 height        = 3
 label         = sub {shift->display_name}
 label density = 50
 bump          = fast
 connector     = dashed
 balloon hover = sub {
                    my $f     = shift;
                    return '' unless $f->type eq 'match';
                    return 'Read: '.$f->display_name.' : '.$f->flag_str;
                }
 key          = Read Pairs

 [Pair:1000]
 feature      = coverage:1001
 glyph        = wiggle_xyplot
 height       = 50
 min_score    = 0
 autoscale    = local

To show alignment data correctly when the user is zoomed in, you should also provide a pointer to the FASTA file containing the reference genome. In this case, modify the db_args line to read:

 db_args       = -bam   /var/www/gbrowse2/databases/bamtest/ex1.bam
                 -fasta /var/www/gbrowse2/databases/bamtest/ex1.fa

SEE ALSO

Bio::Perl, Bio::DB::HTS::Alignment, Bio::DB::HTS::Constants