public class SAMAlignmentMetricsPlugin
Class to read a SAM file, then calculate and print metrics on number of matched-BPs, unmatched-BPs(SNPs), total-aligned bps, insertions, deletions, editDistance, and the total query length. THe total refLength is also included per user request, but this information is not terribly useful. While the query sequence is included in the SAM file, allowing for the readLength to be determined by a seq.length call, the reference sequence is not. The refLen is inferred from the CIGAR string: add all X,EQ,M, D values. This means the refLen is always a total of the TotalBP-Aligned + Total_Deletions.
Entries are filtered to include only primary alignments.
Output: A tab-delimited file with columns for each data point, and rows are the queryName/RNAME pair.
public SAMAlignmentMetricsPlugin(@Nullable
java.awt.Frame parentFrame,
boolean isInteractive)
Class to read a SAM file, then calculate and print metrics on number of matched-BPs, unmatched-BPs(SNPs), total-aligned bps, insertions, deletions, editDistance, and the total query length. THe total refLength is also included per user request, but this information is not terribly useful. While the query sequence is included in the SAM file, allowing for the readLength to be determined by a seq.length call, the reference sequence is not. The refLen is inferred from the CIGAR string: add all X,EQ,M, D values. This means the refLen is always a total of the TotalBP-Aligned + Total_Deletions.
Entries are filtered to include only primary alignments.
Output: A tab-delimited file with columns for each data point, and rows are the queryName/RNAME pair.
public SAMAlignmentMetricsPlugin()
Class to read a SAM file, then calculate and print metrics on number of matched-BPs, unmatched-BPs(SNPs), total-aligned bps, insertions, deletions, editDistance, and the total query length. THe total refLength is also included per user request, but this information is not terribly useful. While the query sequence is included in the SAM file, allowing for the readLength to be determined by a seq.length call, the reference sequence is not. The refLen is inferred from the CIGAR string: add all X,EQ,M, D values. This means the refLen is always a total of the TotalBP-Aligned + Total_Deletions.
Entries are filtered to include only primary alignments.
Output: A tab-delimited file with columns for each data point, and rows are the queryName/RNAME pair.
@Nullable
public net.maizegenetics.plugindef.DataSet processData(@Nullable
net.maizegenetics.plugindef.DataSet input)
public void getReadCountFromSam(@NotNull
java.lang.String samFile)
@Nullable public javax.swing.ImageIcon getIcon()
@NotNull public java.lang.String getButtonName()
@NotNull public java.lang.String getToolTipText()
@NotNull public java.lang.String samFile()
Name of the SAM/BAM file to process.
@NotNull public SAMAlignmentMetricsPlugin samFile(@NotNull java.lang.String value)
Set SAM/BAM to process. Name of the SAM/BAM file to process.
value - SAM/BAM to process@NotNull public java.lang.String outputFile()
File where metrics will be written.
@NotNull public SAMAlignmentMetricsPlugin outputFile(@NotNull java.lang.String value)
Set Directory to write out statistics files.. File where metrics will be written.
value - Directory to write out statistics files.