# HG changeset patch # User chrisw # Date 1574140893 0 # Node ID 8e9a8987581c21a58b2c3774d04ea087dbdfc977 # Parent cb4c1efac7afee504904eb83e0fe29e5fbff91aa Uploaded diff -r cb4c1efac7af -r 8e9a8987581c tool_dependencies.26.xml --- /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 @@ + + + + + + + + https://github.com/BenLangmead/bamcount/releases/download/0.2.6/bamcount-0.2.6.zip + + . + $INSTALL_DIR + + + + $INSTALL_DIR + + + + [options] + +Options: + -h --help Show this screen. + --version Show version. + --threads # of threads to do BAM decompression + +Non-reference summaries: + --alts Print differing from ref per-base coverages + Writes to a CSV file .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 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 .auc.tsv + --bigwig Output coverage as BigWig file(s). Writes to .all.bw + (also .unique.bw when --min-unique-qual is specified). + Requires libBigWig. + --annotation + Path to BED file containing list of regions to sum coverage over + (tab-delimited: chrm,start,end) + --min-unique-qual + 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: .starts.tsv, .ends.tsv + --frag-dist Print fragment length distribution across the genome + Writes to a TSV file .frags.tsv + --echo-sam Print a SAM record for each aligned read + --ends Report end coordinate for each read (useful for debugging) + ]]> + + diff -r cb4c1efac7af -r 8e9a8987581c tool_dependencies.xml --- 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 @@ - https://github.com/ChristopherWilks/bamcount/releases/download/0.4.0/bamcount-0.4.0.zip + https://github.com/ChristopherWilks/bamcount/releases/download/0.4.0/bamcount . $INSTALL_DIR