Mercurial > repos > chrisw > bamcount_test
changeset 3:f84a4ffe8bd7 draft
Uploaded
author | chrisw |
---|---|
date | Tue, 19 Nov 2019 05:23:19 +0000 |
parents | 8e9a8987581c |
children | bf68642a6d3e |
files | tool_dependencies.26.xml |
diffstat | 1 files changed, 0 insertions(+), 76 deletions(-) [+] |
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--- a/tool_dependencies.26.xml Tue Nov 19 05:21:33 2019 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,76 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> -<!-- - <package name="htslib" version="1.9"/> - <package name="libbigwig" version="0.4.2"/> ---> - <package name="bamcount" version="0.2.6"> - <install version="1.0"> - <actions_group> - <actions architecture="x86_64" os="linux"> - <action type="download_by_url">https://github.com/BenLangmead/bamcount/releases/download/0.2.6/bamcount-0.2.6.zip</action> - <action type="move_directory_files"> - <source_directory>.</source_directory> - <destination_directory>$INSTALL_DIR</destination_directory> - </action> - </actions> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> - </action> - </actions_group> - </install> - <readme><![CDATA[ -bamcount 0.2.6 - -BAM and BigWig utility. - -Usage: - bamcount <bam> [options] - -Options: - -h --help Show this screen. - --version Show version. - --threads # of threads to do BAM decompression - -Non-reference summaries: - --alts <prefix> Print differing from ref per-base coverages - Writes to a CSV file <prefix>.alts.tsv - --include-softclip Print a record for soft-clipped bases - --include-n Print mismatch records when mismatched read base is N - --print-qual Print quality values for mismatched bases - --delta Print POS field as +/- delta from previous - --require-mdz Quit with error unless MD:Z field exists everywhere it's - expected - --no-head Don't print sequence names and lengths in header - -Coverage and quantification: - --coverage Print per-base coverage (slow but totally worth it) - --auc <prefix> Print per-base area-under-coverage, will generate it for the genome - and for the annotation if --annotation is also passed in - Writes to a TSV file <prefix>.auc.tsv - --bigwig <prefix> Output coverage as BigWig file(s). Writes to <prefix>.all.bw - (also <prefix>.unique.bw when --min-unique-qual is specified). - Requires libBigWig. - --annotation <bed> <prefix> - Path to BED file containing list of regions to sum coverage over - (tab-delimited: chrm,start,end) - --min-unique-qual <int> - Output second bigWig consisting built only from alignments - with at least this mapping quality. --bigwig must be specified. - Also produces second set of annotation sums based on this coverage - if --annotation is enabled - --double-count Allow overlapping ends of PE read to count twice toward - coverage - --num-bases Report total sum of bases in alignments processed (that pass filters) - -Other outputs: - --read-ends Print counts of read starts/ends, if --min-unique-qual is set - then only the alignments that pass that filter will be counted here - Writes to 2 TSV files: <prefix>.starts.tsv, <prefix>.ends.tsv - --frag-dist <prefix> Print fragment length distribution across the genome - Writes to a TSV file <prefix>.frags.tsv - --echo-sam Print a SAM record for each aligned read - --ends Report end coordinate for each read (useful for debugging) - ]]></readme> - </package> -</tool_dependency>