Lance Parsons
5bbb432cd8
Removed uneccessary hide_stderr.py script from samtools
2011-12-22 11:16:28 -05:00
Lance Parsons
98cdf4c33e
Merged sam_merge fixes from galaxy-central keeping change to set TMP_DIR
2011-12-22 11:13:07 -05:00
Nate Coraor
03c4fa3689
The upload tool requires samtools to upload BAM files, the Pileup tool requires samtools <= 0.1.16.
2011-12-06 11:42:12 -05:00
Daniel Blankenberg
c1dd3d3eaa
Update help for some SAMTools.
2011-11-21 16:55:16 -05:00
Daniel Blankenberg
8986dc2c81
Add SAMTools mpileup.
2011-11-21 16:30:34 -05:00
Daniel Blankenberg
1143dfe2ba
Have Picard MergeSamFiles use return code to determine tool error.
2011-10-27 10:54:42 -04:00
Daniel Blankenberg
8e10b7d6fb
Allow Picard based Merge BAM Files tool to work on sam inputs as well as the previously accepted bam.
2011-10-26 16:03:47 -04:00
Daniel Blankenberg
fc156c89a0
"Merge BAM Files" under SAM Tools section(???) calls Picard MergeSamFiles.jar. Update to new jar location.
2011-10-26 13:35:17 -04:00
Lance Parsons
1669d45d6b
sam_merge: set TMP_DIR and check exit status
2011-10-03 16:59:07 -04:00
Daniel Blankenberg
06ca4ce6a3
Update tests for samtools rmdup.
2011-09-01 09:38:16 -04:00
Daniel Blankenberg
d3ef713d9b
Add samtools rmdup tool.
2011-08-31 16:50:58 -04:00
Kanwei Li
1502eed32f
sam2interval: Add read_name column
2011-08-24 16:43:02 -04:00
Kanwei Li
ad24f8c1dc
Fix sam2interval.py bug due to tab spacing
2011-08-24 13:14:49 -04:00
Ross Lazarus
4720488fa4
Increase lines_diff so sam_merge tests might pass on buildbot
2011-08-04 16:55:13 +10:00
Ross Lazarus
11220e196c
sam_merge.xml tweaks: changed call to MergeSamFiles to use minimal command line flags and finally got LENIENT validation stringency to actually work
2011-08-04 16:50:22 +10:00
Ross Lazarus
5b2e7947ea
Fixed sam_merge.xml to call Picard MergeSamFiles.jar so metadata can be propagated through to the new merged bam from all the individual files - the samtools version of merge would require this to be done separately and passed in with the -h option whereas Picard does it automatically. Added one more test. Interesting that the test for that tool has been failing to correctly pass metadata but passing the buildbot anyway. Thanks to Camille Stephan for pointing out the bug.
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Changes to rgManQQ so the user can obtain a decent pdf image. When millions of points are plotted, these are humongous so GS is called to compress the resulting pdf and they are now of reasonable size. PDF's are now linked from the thumbnails. Some minor fiddling with point size on the Manhatten plots so the intersting ones are a little more obvious.
Minor tweak to twilltestcase.py so composite file components are copied correctly to the directory specified by GALAXY_TEST_SAVE. This makes updating test artefacts much simpler because running tests with GALAXY_TEST_SAVE pointing somewhere will now save every tested output file.
2011-08-04 12:43:30 +10:00
Ross Lazarus
d53c3e984f
Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository
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This is a backout of commit 5765
2011-07-06 09:44:56 +10:00
Ross Lazarus
86b55bb0c0
branch merge
2011-07-05 12:40:43 +10:00
Anton Nekrutenko
87e4ce0100
Fix to sam2interval bug reported by Kathy So. The bug was causing sam2interval to successfully parse unmapped sam entries, which have no valid coordinate.
2011-06-10 14:42:41 -04:00
Kelly Vincent
772da79c12
Updated sam-to-bam to properly assign output dbkey; enhanced sam-to-bam and bam-to-sam functional tests
2011-05-09 12:00:05 -04:00
Daniel Blankenberg
22e3e53ce0
Enhance BAM to SAM tool to optionally output headers.
2011-04-18 16:41:51 -04:00
Kelly Vincent
72c21e0067
Removed unnecessary size check on BAM file produce in view step of sam-to-bam
2011-04-08 12:06:28 -04:00
Greg Von Kuster
8ba7de4c8b
Improved checking to determine if a bam file is sorted. If the version of samtools being used is 0.1.13 or newer, determination of bam sorting is now much more robust. Add a new functional test to the test_library_features script that tests uploading a library_dataset (where the file is an unsorted bam file) using a combination of 'upload_paths' and 'link_to_files'. Rename the test-data file previously named 3.bam to now be named 3unsorted.bam to clarify that it is an unsorted bam file.
2011-03-23 12:18:57 -04:00
Nate Coraor
3fc4c7c4f8
Enable the ftype attribute for test outputs, fixes the sam-to-bam test.
2011-03-01 15:46:35 -05:00
Daniel Blankenberg
4eb1b0a79f
Better determination in tests if a provided input is a DataToolParameter to better handle .gz and .zip uploads and allowing uploads from a sub-directory of test-data/.
2011-02-28 12:16:28 -05:00
Daniel Blankenberg
0ee635749d
Change output format of samtools flagstat from 'text' to 'txt'.
2011-01-26 15:45:27 -05:00
Kelly Vincent
8c13d8e6e8
Corrected output labels to be in line with other tools for NGS tools: sam_to_bam, sam_merge, sam_pileup, bam_to_sam, PerM, bowtie_color_wrapper, bowtie_wrapper, bwa_wrapper, lastz_paired_reads_wrapper, lastz_wrapper, srma_wrapper
2011-01-12 13:31:04 -05:00
Daniel Blankenberg
2a510df4aa
Add samtools flagstat tool.
2010-12-15 23:39:16 -05:00
Kanwei Li
2d0b8eb830
Adjust image links in tools to work with a proxy prefix [Brad Chapman]. Fixes #141
2010-12-14 14:22:13 -05:00
Kelly Vincent
f61d147034
Added --max and --un file output options to Bowtie and modified tests to test for them.
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Made Bowtie test files longer (more than one test read).
Added explanation of canonical and full reference genome variants to BWA and Bowtie.
Added informative labels to output files for NGS tools.
2010-12-01 10:54:35 -05:00
Kelly Vincent
d149382f05
Added version info to stdout for NGS tools
2010-11-24 12:35:49 -05:00
Kanwei Li
ba597f99d7
Refactor sam_bitwise_flag_filter tool, simplifying it and making it faster, especially when there are multiple flag criteria
2010-11-13 14:37:26 -05:00
Dannon Baker
988d94f2d4
Minimally functional splitting.
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Disabled by default, not advisable to enable on a production server (or main!) until scheduling issues are looked at and performance analysis has been done.
Tested 'basic' splitting with many basic tools (bowtie, bwa, filter sam, others). This style of splitting should work for most 'embarassingly parallel' one input, one output tools (no dependence between parallel tasks).
2010-11-10 12:06:05 -05:00
Kelly Vincent
ab1e01e928
Updated Samtools test files to work with version 0.1.9 and cleaned up some formatting and comments in the wrappers
2010-11-08 15:00:54 -05:00
Nate Coraor
ea320b845b
Remove imports of the sets module, set has been a standard type since 2.4. There are more in tools, but they check for the existence of set() first, so will not raise a warning.
2010-09-27 21:35:03 -04:00
James Taylor
e2ae2c4a75
Requirements tags for some samtools tools
2010-09-26 18:06:01 -04:00
Kelly Vincent
33bd292e41
Added BAM-to-SAM tool
2010-09-01 09:44:12 -04:00
Kelly Vincent
5c546a21b3
Updating sam_indel_filter tool; adding NGS: Indel Analysis section; adding indel_analysis, indel_table, and indel_sam2interval tools
2010-07-14 01:09:52 -04:00
Kelly Vincent
862531e04e
Changed the way sam_indel_filter expects quality score cutoffs and fixed bug so it checks qualities for correct bases in all cases
2010-06-24 13:43:38 -04:00
Kelly Vincent
7373e78cd4
Fixed handling of alignments with CIGAR strings with multiple indels for SAM indel filter, plus updated test files
2010-06-10 13:19:43 -04:00
Kelly Vincent
78b17cbb9c
Adding SAM indel filter tool with test files
2010-06-07 15:23:32 -04:00
Kelly Vincent
139c2cf667
Change the way size of output file determined in Bowtie and SAM-to_BAM to deal with memory limitation.
2010-04-30 15:27:41 -04:00
Anton Nekrutenko
008cc9a012
changes to help text
2010-04-15 11:10:57 -04:00
Anton Nekrutenko
254ad33d95
Fixed indel calling in pileup wrapper. TO DO: Write a separate wrapper for indels only.
2010-04-14 13:52:35 -04:00
Kelly Vincent
eeca0c723a
Updated NGS tools' stderr handling to use file rather than pipe to allow for large stderr output
2010-04-12 15:56:13 -04:00
Anton Nekrutenko
04ed0933cf
Updated output format for solid2fastq converter
2010-04-07 08:44:57 -04:00
Kanwei Li
0952b28502
Sync hashbangs
2010-04-01 20:36:31 -04:00
Kelly Vincent
38ad670389
Updated several NGS tools to better handle stderr (allow for extremely large stderr output)
2010-03-30 16:33:19 -04:00
Kelly Vincent
44fb42f6a0
Fix try-except-finally bug to be compatible with Python 2.4 in several tools and twilltestcase.py. Updated liftOver test to replace hard-coded (incorrect) path and modified code file to allow for new path. Improved bowtie error handling.
2010-03-10 11:51:00 -05:00
Anton Nekrutenko
175c63e0fd
Modifications to pileup_parser
2010-03-02 16:35:21 -05:00
Lance Parsons