Mercurial > repos > chrisw > bamcount_test
changeset 2:8e9a8987581c draft
Uploaded
| author | chrisw |
|---|---|
| date | Tue, 19 Nov 2019 05:21:33 +0000 |
| parents | cb4c1efac7af |
| children | f84a4ffe8bd7 |
| files | tool_dependencies.26.xml tool_dependencies.xml |
| diffstat | 2 files changed, 77 insertions(+), 1 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.26.xml Tue Nov 19 05:21:33 2019 +0000 @@ -0,0 +1,76 @@ +<?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>
--- a/tool_dependencies.xml Tue Nov 19 02:55:42 2019 +0000 +++ b/tool_dependencies.xml Tue Nov 19 05:21:33 2019 +0000 @@ -8,7 +8,7 @@ <install version="1.0"> <actions_group> <actions architecture="x86_64" os="linux"> - <action type="download_by_url">https://github.com/ChristopherWilks/bamcount/releases/download/0.4.0/bamcount-0.4.0.zip</action> + <action type="download_by_url">https://github.com/ChristopherWilks/bamcount/releases/download/0.4.0/bamcount</action> <action type="move_directory_files"> <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR</destination_directory>