given a set of genomic intervals #if $maf_source_type.maf_source == "user" #interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --mafIndex=$maf_source_type.maf_file.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} #else #interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_identifier --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} #end if# --overwrite_with_gaps=$overwrite_with_gaps Locally Cached Alignments Alignments in Your History No Yes

**What it does** A single genomic region can be covered by multiple alignment blocks. In many cases it is desirable to stitch these alignment blocks together. This tool accepts a list of genomic intervals. For every interval it performs the following: * finds all MAF blocks that overlap the interval; * sorts MAF blocks by alignment score; * stitches blocks together and resolves overlaps based on alignment score; * outputs alignments in FASTA format. ------ **Example** Here three MAF blocks overlapping a single interval are stitched together. Space between blocks 2 and 3 is filled with gaps: .. image:: ../static/images/maf_icons/stitchMaf.png