| Fix bug #69 by increasing the sensitivity of long-read (consensus sequence) alignment, decreasing the mismatch penalty to 1 from default 3 |
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almost 11 years ago
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| Add option to remove alignment gaps '~' in the filtered consensus sequence; fixes bug #67 where deletions are replaced with 'N' but not removed so truncated alleles are not interpreted properly |
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almost 11 years ago
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| Merge pull request #66 from janders3-nmdp/samplecount_v_processorcount_disparity_fix |
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almost 11 years ago
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| improved splitting algorithm for BSD-derived Unix operating systems |
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almost 11 years ago
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| Merge pull request #62 from janders3-nmdp/rhel_osx_support_for_splitter.bash |
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almost 11 years ago
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| Merge pull request #64 from janders3-nmdp/boilerplate_creation |
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almost 11 years ago
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| fixes to boilerplate creation, should resolve issue #63 |
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almost 11 years ago
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| Merge github.com:nmdp-bioinformatics/pipeline into rhel_osx_support_for_splitter.bash |
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almost 11 years ago
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| Merge pull request #57 from ckennedy-nmdp/bug56 |
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almost 11 years ago
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| Take Michael's suggestion and use '\s+' to split -- simpler, better |
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almost 11 years ago
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| Fix bug #56, which is caused by improper formatting of regions files for filtering -- in this case spaces instead of tabs between index and coordinate fields produced an ArrayOutOfBoundsException. Sometimes formatting issues arise when copying files around. I put an error message into the code (Mark will have to reformat the regions files in /mnt/common/) |
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almost 11 years ago
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| Merge pull request #55 from ckennedy-nmdp/fix-bug-41 |
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almost 11 years ago
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| Fix issue #41 -- reverse complement minus strand HLA genes so they can be properly interpreted. Warning: this is a hack and should be replaced with properly configured tool where filtered regions include the strand (a la GFF or HML) |
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almost 11 years ago
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| some in-progress enhancements to splitter to handle osx, redhat, and soon, to deal with single-core machines and single-sample runs |
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almost 11 years ago
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| Merge pull request #48 from janders3-nmdp/lowram_warning |
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almost 11 years ago
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| documentation/warning updates |
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almost 11 years ago
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| Merge pull request #40 from ckennedy-nmdp/process-labcorp-data |
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almost 11 years ago
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| Redirect mpileup (reads) output to file |
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almost 11 years ago
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| Merge pull request #38 from janders3-nmdp/less_dumb_fastq_check |
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almost 11 years ago
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| now splitter will find fastq files in subdirs at preliminary check |
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almost 11 years ago
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| Merge pull request #35 from mheuer-nmdp/travis-badge |
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almost 11 years ago
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| Merge pull request #33 from mheuer-nmdp/travis-configuration |
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almost 11 years ago
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| Merge pull request #31 from warrenlr/patch-1 |
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almost 11 years ago
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| Update process_fastq.bash |
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almost 11 years ago
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| adding Travis CI badge to readme |
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almost 11 years ago
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| adding Travis CI configuration with no-op build script |
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almost 11 years ago
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| Merge pull request #28 from janders3-nmdp/user_specific_tmpdir |
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almost 11 years ago
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| do notuse system /tmp, user ~/tmp |
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almost 11 years ago
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| Merge pull request #22 from mheuer-nmdp/update-htsjdk |
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almost 11 years ago
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| Merge pull request #24 from ckennedy-nmdp/test-branch |
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almost 11 years ago
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