# 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