hoffmangroup / genomedata

The Genomedata format for storing large-scale functional genomics data.

https://genomedata.hoffmanlab.org/

GNU General Public License v2.0

2 stars 1 forks source link

Wiggle parsing does not support comment or browser lines #4

Open EricR86 opened 10 years ago

EricR86 commented 10 years ago

Original report (archived issue) by Eric Roberts (Bitbucket: ericr86, GitHub: ericr86).

From Google Code Issue #14

Imported Labels: bug, imported, Priority-Medium

From orion.bu...@gmail.com on March 16, 2010 17:09:50

The wiggle parsing code in genomedata_load_data.c assumes the wiggle file will start with variableStep or fixedStep. The wiggle spec states that the first line must be a track definition line. If a standard wiggle file is presented, the loader will default to reading it in BED format and throw a large number of errors.

Original issue: http://code.google.com/p/genomedata/issues/detail?id=14

EricR86 commented 10 years ago

Original comment by Eric Roberts (Bitbucket: ericr86, GitHub: ericr86).

From orion.bu...@gmail.com on March 16, 2010 14:33:05

Here are the first 15 lines from the file. This was downloaded directly from UCSC:

track type=wiggle_0 name="Tag Counts" description="UW Footprints Tag Counts"

output date: 2010-03-15 19:17:44 UTC

chrom specified: chr1

position specified: 1-230208

This data has been compressed with a minor loss in resolution.

(Worst case: 3.41406) The original source data

(before querying and compression) is available at

http://hgdownload.cse.ucsc.edu/downloads.html variableStep chrom=chr1 span=1

12 9.89764 13 19 14 7.88976 15 2 16 11.9055 34 4.77953

EricR86 commented 10 years ago

Original comment by Eric Roberts (Bitbucket: ericr86, GitHub: ericr86).

From hoffman...@gmail.com on March 16, 2010 14:47:54

While you're at it, you might as well code in ignoring browser lines. http://genome.ucsc.edu/goldenPath/help/customTrack.html#BROWSER

EricR86 commented 10 years ago

Original comment by Eric Roberts (Bitbucket: ericr86, GitHub: ericr86).

From hoffman...@gmail.com on August 14, 2010 09:33:11

Genomedata 1.2.2 now accepts track lines. Comment lines and browser lines are not yet accepted.

Status: Accepted
Owner: hoffman.mm
Labels: -Priority-High Priority-Medium

EricR86 commented 10 years ago

Original comment by Eric Roberts (Bitbucket: ericr86, GitHub: ericr86).

changed priority from "trivial" to "minor"
Edited issue description* changed kind from "bug" to "enhancement"
set assignee_account_id to "557058:c80ca578-03a1-4ac6-b3ee-50372a3fceee"
set assignee to "ericr86 (Bitbucket: ericr86, GitHub: ericr86)"

EricR86 commented 10 years ago

Original comment by Michael Hoffman (Bitbucket: hoffman, GitHub: michaelmhoffman).

changed title from "Wiggle parsing does not conform to spec" to "Wiggle parsing does not support comment or browser lines"