net.maizegenetics.pangenome.hapCalling

Class SAMMetricsPlugin

net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin

public class SAMMetricsPlugin

Plugin to extract metrics from SAM file(s) related to alignment quality. Summary statistics are written to a tab-delimited file with one row for each input SAM file, and include: number of mapped and unmapped reads, mean and median alignment edit distances. it also writes one file per input SAM containing the best (lowest) edit distances for each read, separated by new lines

Assumptions: sam/bam files have the optional field "NM", containing the alignment edit distance.

Required input: samDir - directory containing one or more .sam or .bam files outDir - directory in which we will write output files

Optional input: samFile - if only one sam or bam file is to be processed, the name of the file. It should reside in samDir

Output: SAM_summary_statistics.txt - tab-delimited table of summary statistcs SAMPLE_editDistances.txt - file containing the lowest edit distances for each read in SAMPLE.sam. One per sam processed.

Constructor Detail

SAMMetricsPlugin

public SAMMetricsPlugin(@Nullable
                        java.awt.Frame parentFrame,
                        boolean isInteractive)

Plugin to extract metrics from SAM file(s) related to alignment quality. Summary statistics are written to a tab-delimited file with one row for each input SAM file, and include: number of mapped and unmapped reads, mean and median alignment edit distances. it also writes one file per input SAM containing the best (lowest) edit distances for each read, separated by new lines

Assumptions: sam/bam files have the optional field "NM", containing the alignment edit distance.

Required input: samDir - directory containing one or more .sam or .bam files outDir - directory in which we will write output files

Optional input: samFile - if only one sam or bam file is to be processed, the name of the file. It should reside in samDir

Output: SAM_summary_statistics.txt - tab-delimited table of summary statistcs SAMPLE_editDistances.txt - file containing the lowest edit distances for each read in SAMPLE.sam. One per sam processed.

SAMMetricsPlugin

public SAMMetricsPlugin()

Plugin to extract metrics from SAM file(s) related to alignment quality. Summary statistics are written to a tab-delimited file with one row for each input SAM file, and include: number of mapped and unmapped reads, mean and median alignment edit distances. it also writes one file per input SAM containing the best (lowest) edit distances for each read, separated by new lines

Assumptions: sam/bam files have the optional field "NM", containing the alignment edit distance.

Required input: samDir - directory containing one or more .sam or .bam files outDir - directory in which we will write output files

Optional input: samFile - if only one sam or bam file is to be processed, the name of the file. It should reside in samDir

Output: SAM_summary_statistics.txt - tab-delimited table of summary statistcs SAMPLE_editDistances.txt - file containing the lowest edit distances for each read in SAMPLE.sam. One per sam processed.

Method Detail

processData

@Nullable
public net.maizegenetics.plugindef.DataSet processData(@Nullable
                                                                 net.maizegenetics.plugindef.DataSet input)

writeEditDistancesToFile

public void writeEditDistancesToFile(@NotNull
                                     java.util.List<java.lang.Integer> distances,
                                     @NotNull
                                     java.lang.String fileName)

Writes list of ints (edit distances) to a file. Each int gets its own line

getSAMStats

@NotNull
public net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin.AlignmentSummary getSAMStats(@NotNull
                                                                                                     java.io.File samFile)

Given a sam or bam file, return the following as an AlignmentSummary object: number of aligned reads number of unaligned reads list of the minimum edit distance for each aligned read When the sam file contains multiple alignments (i.e. secondary alignments), we get the edit distance for each alignment and then choose the lowest to add to the list.

getIcon

@Nullable
public javax.swing.ImageIcon getIcon()

getButtonName

@NotNull
public java.lang.String getButtonName()

getToolTipText

@NotNull
public java.lang.String getToolTipText()

samFile

@NotNull
public SAMMetricsPlugin samFile(@NotNull
                                         java.lang.String value)

Set sam file. Name of singular sam or bam file to process. Does not include path.

Parameters:

value - sam file

Returns:

this plugin

samDir

@NotNull
public SAMMetricsPlugin samDir(@NotNull
                                        java.lang.String value)

Set sam directory. Path to a directory containing one or more sam/bam files. To be recognized by this plugin, files must end with .sam or .bam All other files in the directory will be ignored.

Parameters:

value - sam directory

Returns:

this plugin

outDir

@NotNull
public java.lang.String outDir()

A directory to which output text files will be written. This includes the summary statistics table as well as a file of minumum edit distances for each sam/bam file processed.

Returns:

output directory

outDir

@NotNull
public SAMMetricsPlugin outDir(@NotNull
                                        java.lang.String value)

Set the output directory. A directory to which output text files will be written. This includes the summary statistics table as well as a file of minumum edit distances for each sam/bam file processed.

Parameters:

value - output directory

Returns:

this plugin