oicr-gsi/debarcer issues and pull requests

#223 - Rjdev

Pull Request - State: closed - Opened by rjovelin almost 4 years ago - 1 comment

#222 - Rjdev

Pull Request - State: closed - Opened by rjovelin over 4 years ago

#221 - re-packaging

Pull Request - State: closed - Opened by rjovelin over 4 years ago

#220 - Move argument parsing to main-function

Pull Request - State: closed - Opened by FelixMoelder over 4 years ago - 1 comment

#219 - Rjdev

Pull Request - State: closed - Opened by rjovelin over 4 years ago

#218 - Rjdev

Pull Request - State: closed - Opened by rjovelin over 4 years ago

#217 - Missing records for different family size in merged consensus file

Issue - State: closed - Opened by rjovelin over 4 years ago
Labels: bug

#216 - Rjdev

Pull Request - State: closed - Opened by rjovelin over 4 years ago

#215 - Rjdev

Pull Request - State: closed - Opened by rjovelin over 4 years ago

#214 - Rjdev

Pull Request - State: closed - Opened by rjovelin over 4 years ago

#213 - Rjdev

Pull Request - State: closed - Opened by rjovelin almost 5 years ago

#212 - Rjdev

Pull Request - State: closed - Opened by rjovelin almost 5 years ago

#211 - run debarcer on SGE or Univa. fixed issue #209

Pull Request - State: closed - Opened by rjovelin almost 5 years ago

#210 - add UMI separator parameter. fixed issue #201

Pull Request - State: closed - Opened by rjovelin almost 5 years ago

#209 - Allow jobs to run on univa

Issue - State: closed - Opened by rjovelin almost 5 years ago
Labels: enhancement

#208 - Rjdev

Pull Request - State: closed - Opened by rjovelin almost 5 years ago

#207 - edited required modules

Pull Request - State: closed - Opened by rjovelin almost 5 years ago

#206 - Debarcer group function does not check for empty regions

Issue - State: closed - Opened by prisnir-zz almost 5 years ago - 3 comments
Labels: enhancement

#205 - Issues with debarcer "group" function in creating new output directory

Issue - State: closed - Opened by prisnir-zz almost 5 years ago
Labels: bug

#204 - Keep network plot?

Issue - State: closed - Opened by rjovelin almost 5 years ago - 1 comment
Labels: enhancement

#203 - Keep network plot?

Issue - State: closed - Opened by rjovelin almost 5 years ago - 1 comment
Labels: enhancement

#202 - Add base quality filter

Issue - State: closed - Opened by rjovelin almost 5 years ago
Labels: enhancement

#201 - Add parameter to specify UMI separator

Issue - State: closed - Opened by rjovelin almost 5 years ago
Labels: enhancement

#200 - Rjdev

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#199 - fixed readme extension

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#198 - fixed readme extension

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#197 - updated required modules

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#196 - updated required modules

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#195 - Rjdev

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#194 - include md files

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#193 - Rjdev

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#192 - Rjdev2

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#191 - Rjdev2

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#190 - removed file

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#189 - Rjdev

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#188 - Rjdev2

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#187 - Rjdev2

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#186 - Verify read depth of the regions identified by the scanner

Issue - State: closed - Opened by rjovelin about 5 years ago - 1 comment

#185 - Fix tick positions

Issue - State: closed - Opened by rjovelin about 5 years ago

#184 - AssertionError in VCF call

Issue - State: closed - Opened by rjovelin about 5 years ago - 1 comment
Labels: bug

#183 - KeyError in VCF Call

Issue - State: closed - Opened by rjovelin about 5 years ago - 1 comment
Labels: bug

#182 - Unexpected values in yaml

Issue - State: closed - Opened by rjovelin about 5 years ago - 1 comment
Labels: bug

#181 - Ref base not defined

Issue - State: closed - Opened by rjovelin about 5 years ago - 2 comments
Labels: bug

#180 - Issue when computing tick positions

Issue - State: closed - Opened by rjovelin about 5 years ago - 1 comment
Labels: bug

#179 - KeyError because of missing position during plotting

Issue - State: closed - Opened by rjovelin about 5 years ago - 1 comment
Labels: bug

#178 - Assertion error in Collapse

Issue - State: closed - Opened by rjovelin about 5 years ago - 1 comment
Labels: bug

#177 - Rjdev2

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#176 - Read1 is cropped for sureselect and haloplex libraries

Issue - State: closed - Opened by rjovelin about 5 years ago - 2 comments
Labels: bug

#175 - use collections to speed up counting umi sequences

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#174 - write filtered reads to fastqs

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#173 - Rjdev2

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#172 - do not write VCF if there is no records

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#171 - fixed chromosome names

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#170 - Rjdev2

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#169 - fixed issue #167

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#168 - Output preprocessing-filtered reads to fastqs

Issue - State: closed - Opened by rjovelin about 5 years ago

#167 - Umis in paired reads

Issue - State: closed - Opened by rjovelin about 5 years ago
Labels: bug

#166 - VCF output

Issue - State: closed - Opened by rjovelin about 5 years ago

#165 - enclose sample parameter in double quotes

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#164 - Rjdev2

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#163 - Rjdev2

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#162 - Phred score is set to 0

Issue - State: closed - Opened by rjovelin about 5 years ago - 1 comment
Labels: enhancement

#161 - Rjdev2

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#160 - Rjdev2

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#159 - Rjdev2

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#158 - Rjdev2

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#157 - Rjdev2

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#156 - Rjdev2

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#155 - Update functions that read consensus files

Issue - State: closed - Opened by rjovelin about 5 years ago - 2 comments

#154 - Rjdev2

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#153 - Rjdev2

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#152 - Rjdev2

Pull Request - State: closed - Opened by rjovelin about 5 years ago

#151 - Output bam with consensus reads

Issue - State: closed - Opened by rjovelin over 5 years ago - 1 comment
Labels: enhancement

#150 - Reference base is not defined

Issue - State: closed - Opened by rjovelin over 5 years ago - 1 comment

#149 - Rjdev2

Pull Request - State: closed - Opened by rjovelin over 5 years ago

#148 - Improve allelic counts

Issue - State: closed - Opened by rjovelin over 5 years ago - 1 comment

#147 - No need to loop through interval positions. Positions already keys in dictionary

Issue - State: closed - Opened by rjovelin over 5 years ago

#146 - preprocessing

Issue - State: closed - Opened by rjovelin over 5 years ago - 2 comments

#145 - Check that indel sequence is correct

Issue - State: closed - Opened by rjovelin over 5 years ago - 1 comment
Labels: question

#144 - Exclude filtered reads when computing read depth

Issue - State: closed - Opened by rjovelin over 5 years ago - 1 comment

#143 - plot option not available from the run module

Issue - State: closed - Opened by rjovelin over 5 years ago - 1 comment

#142 - overlapping labels in donut plot

Issue - State: closed - Opened by rjovelin over 5 years ago - 1 comment

#141 - generate a single VCF per consensus file

Issue - State: closed - Opened by rjovelin over 5 years ago - 1 comment

#140 - filter secondary and supplementary alignments

Issue - State: closed - Opened by rjovelin over 5 years ago - 1 comment

#139 - VCF output

Issue - State: closed - Opened by rjovelin over 5 years ago

#138 - pysam and samtools give slightly different allele count and read depth

Issue - State: closed - Opened by rjovelin over 5 years ago - 1 comment

#137 - unmapped reads

Issue - State: closed - Opened by rjovelin over 5 years ago - 1 comment

#136 - Add indel sequences to VCF

Issue - State: closed - Opened by rjovelin over 5 years ago - 1 comment
Labels: enhancement

#135 - Add parameter for filter

Issue - State: closed - Opened by rjovelin over 5 years ago - 1 comment

#134 - Extend debarcer to other library preps

Issue - State: closed - Opened by rjovelin over 5 years ago - 1 comment

#133 - Add option to locate umi within reads

Issue - State: closed - Opened by rjovelin over 5 years ago - 1 comment

#132 - Restrict reads to the genomic interval during umi family grouping

Issue - State: closed - Opened by rjovelin over 5 years ago - 1 comment

#131 - Restrict positions to genomic interval

Issue - State: closed - Opened by rjovelin over 5 years ago - 1 comment

#130 - use pysam to extract reference positions/sequence

Issue - State: closed - Opened by rjovelin over 5 years ago
Labels: enhancement

#129 - Ref_threshold and all_threshold

Issue - State: closed - Opened by rjovelin over 5 years ago - 1 comment
Labels: question

#121 - off by one error in the cons file

Issue - State: closed - Opened by lheisler over 5 years ago - 3 comments

#118 - Missing argument

Issue - State: closed - Opened by rjovelin over 5 years ago - 1 comment

#94 - Deletion call error

Issue - State: closed - Opened by qingzhou1 almost 6 years ago - 6 comments

#90 - add functionality to identify regions of coverage

Issue - State: closed - Opened by lheisler over 6 years ago - 1 comment
Labels: enhancement

#71 - Add configuration for consensus calling parameters

Issue - State: closed - Opened by pmkrzyzanowski over 8 years ago

GitHub / oicr-gsi/debarcer issues and pull requests