\name{bam_tally-methods}
 \docType{methods}
 \alias{bam_tally-methods}
 \alias{bam_tally,BamFile-method}
 \alias{bam_tally,character-method}
 \alias{bam_tally,GmapBamReader-method}

 \alias{genome,TallyIIT-method}

 \alias{bam_tally}

 \alias{variantSummary}

 \title{Per-position Alignment Summaries}
 

 \description{
   Given a set of alignments, for each position in the genome output
   counts for the reference allele and all alternate alleles. Often used
   as a precursor to detecting variants. Indels will be supported soon.
 }
 
 \usage{

 \S4method{bam_tally}{BamFile}(x, param, ...)
 \S4method{bam_tally}{character}(x, param, ...)

 variantSummary(x, read_pos_breaks = NULL,
                keep_ref_rows = FALSE, read_length = NA_integer_,
                high_nm_score = NA_integer_)

 }
 
 \arguments{
   \item{x}{a \code{BamFile} object or string path to a BAM file to read}

   \item{param}{The \code{\linkS4class{BamTallyParam}} object with

     parameters for the tally operation. }

   \item{read_pos_breaks}{The breaks, like those passed to \code{\link{cut}}
     for aggregating the per-read position counts. If \code{NULL}, no per-cycle
     counts are returned.}
   \item{keep_ref_rows}{Whether to keep the rows describing only the
     reference calls, i.e., where ref and alt are the same. These are
     useful when one needs the reference counts even when there are no
     alts at that position.}

   \item{read_length}{The expected read length. If the read length is NA,
     the MDFNE (median distance from nearest end) statistic will NOT be
     calculated.}

   \item{high_nm_score}{The value at which an NM value is considered high.}

   \item{...}{Arguments that override settings in \code{param}.}
 }
 
 \value{

   The \code{bam_tally} function returns an opaque pointer to a C-level
   data structure with the class \dQuote{TallyIIT}. Currently, the only
   operation applicable to this object is \code{variantSummary}.
   
   The \code{variantSummary} function returns
   a \code{\link[VariantAnnotation]{VRanges}}, with a range for each position
   that passed the filters. The depth columns correspond to the counts
   after quality filtering (except for indels, for which there is no
   quality filtering). The following \code{elementMetadata}
   columns are also present:

   \item{n.read.pos}{The number of unique read positions for the alt allele.}
   \item{n.read.pos.ref}{The number of unique read positions for the ref allele.}

   \item{raw.count.total}{The total number of reads at that position,

     including reference and all alternates.}

   \item{count.plus}{The number of positive strand reads for the alternate

     allele, \code{NA} for the reference allele row.}

   \item{count.plus.ref}{The number of positive strand reads for the reference

     allele.}

   \item{count.minus}{The number of negative strand reads for the alternate

     allele, \code{NA} for the reference allele row.}

   \item{count.minus.ref}{The number of negative strand reads for the reference

     allele.}

   \item{count.del.plus}{The plus strand deletion count over the
     position.}
   \item{count.del.minus}{The minus strand deletion count over the
     position.}

   \item{read.pos.mean}{Mean read position for the alt allele.}
   \item{read.pos.mean.ref}{Mean read position for the ref allele.}

   \item{read.pos.var}{Variance in the read positions for the alt allele.}
   \item{read.pos.var.ref}{Variance in the read positions for the ref allele.}

   \item{mdfne}{Median distance from nearest end for the alt allele.}
   \item{mdfne.ref}{Median distance from nearest end for the ref allele.}

   \item{count.high.nm}{The number of alt reads with an NM value at or above the
     \code{high_nm_score} cutoff.}
   \item{count.high.nm.ref}{The number of ref reads with an NM value at
     or above the \code{high_nm_score} cutoff.}
   
   If codon counting was enabled, there will be a column giving the codon
   strand: \code{codon.strand}.
   
   If the \code{xs} parameter was \code{TRUE}, there will be four
   additional columns giving the counts by aligner-determined
   strand: \code{count.xs.plus}, \code{count.xs.plus.ref},
   \code{count.xs.minus}, and \code{count.xs.minus.ref}.

   An additional column is present for each bin formed by

   the \code{read_pos_breaks} parameter, with the read count for that bin.

 }
 

 \seealso{\code{tallyVariants} in the VariantTools package provides a
   high-level wrapper for this functionality.}
 

 \author{Michael Lawrence}