Number of processes to split the work between. Use the legacy layout of integer-labeled zoom levels. Include ‘,agg=’ to specify an aggregation function different from ‘sum’. Specify the names of value columns to merge as ‘’. One or more additional base coolers to aggregate from, if needed. balance-args ¶Īdditional arguments to pass to cooler balance -i, -base-uri ¶ Use suffixes B or N to specify a progression: B for binary (geometric steps of factor 2), N for nice (geometric steps of factor 10 interleaved with steps of 2 and 5). Number of pixels allocated to each process -r, -resolutions ¶Ĭomma-separated list of target resolutions.

Number of processes to use for batch processing chunks of pixels -c, -chunksize ¶ All lower-triangle input elements will be discarded! | If you wish to treat lower- and upper-triangle input data as distinct, use the -no-symmetric-upper option instead. duplex: Incoming data contains upper- and lower-triangle duplicates. Execution will be aborted if duplicates are detected. | unique: Incoming data comes from a unique half of a symmetric matrix, regardless of how element coordinates are ordered. comment-char ¶Ĭopy status of input data when using symmetric-upper storage. Pass this flag if the bin IDs listed in a COO file are one-based instead of zero-based. Can also be specified using the –field option. Store the ‘count’ column as floating point values instead of as integers. Also specifies the size of the buffer during the merge step. These chunks will be saved as temporary partial Coolers and merged at the end. Size (in number of lines/records) of data chunks to read and process from the input file at a time. Repeat the -field option for each additional field. Optionally, append : followed by dtype= to specify the data type (e.g. Specify quantitative input fields to aggregate into value columns using the syntax -field =. hg19, mm10) -field ¶Īdd supplemental value fields or override default field numbers for the specified format. ‘bg2’ refers to a 2D bedGraph-like file (chrom1, start1, end1, chrom2, start2, end2, count). ‘coo’ refers to a tab-delimited sparse triplet file (bin1, bin2, count). See for more details.Ĭooler load BINS_PATH PIXELS_PATH COOL_PATH Provide as a comma-separated list of key-value pairs of the form ‘k1=v1,k2=v2,…’. Options to modify the data filter pipeline. Maximum number of chunks to merge before invoking recursive merging -storage-options ¶ no-delete-temp ¶ĭo not delete temporary files when finished. Pass - to use the platform default temp dir. temp-dir ¶Ĭreate temporary files in a specified directory. Passing ‘count’ as the target name will override the default behavior of storing pair counts. float), and/or agg= to specify an aggregation function different from sum (e.g.

All input records that map to the lower triangle will be discarded! | If you wish to treat lower- and upper-triangle input data as distinct, use the -no-symmetric-upper option. | unique: Incoming data comes from a unique half of a symmetric map, regardless of how the coordinates of a pair are ordered. This allows for distinct upper- and lower-triangle values -input-copy-status ¶Ĭopy status of input data when using symmetric-upper storage. N, -no-symmetric-upper ¶Ĭreate a complete square matrix without implicit symmetry. Positions are zero-based -comment-char ¶Ĭomment character that indicates lines to ignore. Number of input lines to load at a time -0, -zero-based ¶ Pos2 field number (one-based) -chunksize ¶ Pos1 field number (one-based) -c2, -chrom2 ¶Ĭhrom2 field number (one-based) -p2, -pos2 ¶ Path to JSON file containing user metadata. See the cooler_cli.ipynb Jupyter Notebook for specific examples on usage: ( ).Ĭooler cload pairs BINS PAIRS_PATH COOL_PATH On error, drop into the post-mortem debugger shell. Generate fragment-delimited genomic bins. Generate a multi-resolution cooler file by coarsening.ĭisplay and browse a cooler with matplotlib.Ĭopy a cooler from one file to another or within the same file.Ĭreate a hard, soft or external link to a cooler. Merge multiple coolers with identical axes. Create a cooler from genomic point pairs and bins.Ĭreate a cooler from a pre-binned matrix.

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