summarizePolishes1

Utilities to work with sim4db-generated alignment files convertpolishes - convert between sim4db and gff3 formats filterpolishes - filter alignments based on sequence identity, coverage and length. mergepolishes - merge alignments from multiple files sortpolishes - sort alignments by cdna or genomic sequence index or sequence name converttoextent - convert from sim4db format to a single-line tab-delimited format fixpolishesiid - updates a sim4db file to use the sequence index of a specific fasta file. can also be used to extract a subset of the alignments from the sim4db file. depthofpolishes - outputs a tab-delimited histogram of the depth of polishes at various window sizes. headpolishes - print the first n alignments in a file, similar to head(1) pickbestpolish - report only the 'best' alignment for each cdna pickuniquepolish - reports alignments where there is a clear single best alignment for each cdna. plotcoveragevsidentity - generates (1) a histogram of the percent identity, (2) a histogram of the percent coverage, and (3) a list of percent identity and coverage (for use in a scatter plot). uniqpolishes - filters out all alignments for cdna with multiple alignments (-uniq) or with a single alignment (-dupl). similar to uniq(1) realignpolishes - recompute the alignments listed in a sim4db file. reportalignmentdifferences - generates a histogram of the types of errors in a set of alignments unsupported and deprecated comparepolishes - correlate alignments in two files. converttoatac - converts from sim4db format to atac format. detectchimera - examines alignments for sequences that might be chimeric. mappedcoverage - reports the amount of the query sequence (est, cdna) that is covered by alignments. parsesnp - analyzes alignments for snps. removeduplicate - searches the input for duplicate alignments. vennpolishes - generates a venn diagram for multiple sim4db files. used internally by estmapper cleanpolishes summarizepolishes