1.40.0 #351

amirshams84 · Jul 7, 2017

Please Please Please
Add Cigar String for compressed alignment on align.seqs alignment report
or please add the ref and query part of the sequence which aligned together
Cigar string like what Bowtie result provide
Ref& Query aligned sequences like BLAST provide

Regards

mothur-westcott	`Adds Boost line to log file`		`6fa006c`
mothur-westcott	`Adding summary class` #319		`cb32bbf`
mothur-westcott	`Working on unit testing`		`08da960`
mothur-westcott	`Adds parallelized summary class` Summaries fasta and count or names file Adds class to summary.seqs #319		`87ea1bb`
mothur-westcott	`Adds summary file to summary class` #319		`2c3bfb4`
mothur-westcott	`Fixes typos in chimera commands help`		`cc6699f`
mothur-westcott	`Fixes make.file bug when full path is used`		`7719df7`
mothur-westcott	`Adds contigsreport parameter to summary.seqs` #319		`6a4070c`
mothur-westcott	`Adds align report parameter to summary.seqs` #319		`cff86ef`
mothur-westcott	`Working on screen.seqs change` #319		`9d46741`
mothur-westcott	`Fixes name mismatch make.contigs gz files` Only caused issue when running gz files with ffastq and rfastq parameters. #320		`33693e5`
mothur-westcott	`Defaults flip=t in align.seqs`		`1b0de01`
mothur-westcott	`Working on google test compile`	All checks have failed 2 errored checks continuous-integration/travis-ci/pr — The Travis CI build could not complete due to an error Details continuous-integration/travis-ci/push — The Travis CI build could not complete due to an error Details	`531c82f`
mothur-westcott	`Merge pull request #322 from mothur/Summary_Class_319` Summary class 319		`497ffff`
mothur-westcott	`Resolved test project linking issues`		`f403a82`
mothur-westcott	`Ignores 'ignore' group in shhh.flows`		`2bf703e`
mothur-westcott	`Allows for multiple char delim in make.contigs`		`9bfdd55`
mothur-westcott	`Removes couts`		`d0615d5`
mothur-westcott	`Removes dependency and simplifies calculator class` #240		`8003738`
mothur-westcott	`Creates fn, fp, fpfn, mcc, ses,spec, tn, tp, tptn classes` #240		`ea7ff2f`
mothur-westcott	`Removes calculator.cpp` #240		`81231f7`
mothur-westcott	`Organizes calcs` #240		`e01fc00`
mothur-westcott	`Fixes printing issue for dereplicate=t`		`e635fc4`
mothur-westcott	`Adds accuracy,f1score,fdr,npv,ppv calcs` #240		`7b8a60b`
mothur-westcott	`Adds ClusterMetric class to cluster commands` #240		`f080a68`
mothur-westcott	`Simplify opticlust source` #240		`c4ed54f`
mothur-westcott	`Hardcodes input files for testing` #196		`51b19f3`
mothur-westcott	`Fakes tp,tn,fp,fn` #196		`a51e42c`
mothur-westcott	`Setup for test cluster calcs` #196		`a9bbfb8`
mothur-westcott	`Reducing dependancies in Testing` #196		`92c5d76`
mothur-westcott	`Test project changes` #196		`506a3e5`
mothur-westcott	`Reduces dependancies TestOptimatrix` #196		`b4a0069`
mothur-westcott	`Minor testing fixes` #196		`b7c27e5`
mothur-westcott	`Fix to compile`		`6b25e3d`
mothur-westcott	`Fix to compile`		`53aafb2`
mothur-westcott	`Reduces log file size in debug mode`		`864e470`
mothur-westcott	`Adds debug to opticlust`		`498fcd7`
mothur-westcott	`Adds fakes for optimatrix` #196		`bb26bf9`
mothur-westcott	`Adds tests for opticluster` #196		`a43397c`
mothur-westcott	`Adds tests for cluster calcs` #196		`7159150`
mothur-westcott	`Simplifies trimOligos constructor` #240		`20d167e`
mothur-westcott	`Working on adding fakeOligos` #196	All checks have passed 2 successful checks continuous-integration/travis-ci/pr — The Travis CI build passed Details continuous-integration/travis-ci/push — The Travis CI build passed Details	`03d92cb`
mothur-westcott	`Opti Improvements` #330		`3b0c70f`
mothur-westcott	`WIP shared file data structure upgrade` #240		`2ad9cd3`
mothur-westcott	`Removes couts` #240		`998c363`
mothur-westcott	`Abort cluster if incorrect files for method` #240		`d780be0`
mothur-westcott	`Adds opti method to mgcluster` #342		`d46aceb`
mothur-westcott	`Code Cleanup` #240	All checks have passed 2 successful checks continuous-integration/travis-ci/pr — The Travis CI build passed Details continuous-integration/travis-ci/push — The Travis CI build passed Details	`1971ad9`
mothur-westcott	`Merge branch 'mgcluster_opti_342' into 1.40.0`		`207f145`
mothur-westcott	`Conflict resolution` #342		`2ef4e6c`
mothur-westcott	`Adds -03 to project`	All checks have passed 2 successful checks continuous-integration/travis-ci/pr — The Travis CI build passed Details continuous-integration/travis-ci/push — The Travis CI build passed Details	`82e6259`
mothur-westcott	`Merge branch '1.40.0' into opti_improvements2`		`3e27e6f`
mothur-westcott	`Merge in 1.40.0 changes and resolve conflicts`		`ea71db7`
mothur-westcott	`Rewrite of shared file data structure` #347 #240		`b86b3e2`
mothur-westcott	`Bug Fix: start trimming extra base pcr.seqs` #348	All checks have passed 2 successful checks continuous-integration/travis-ci/pr — The Travis CI build passed Details continuous-integration/travis-ci/push — The Travis CI build passed Details	`232c6f5`
mothur-westcott	`Make.sra - remove trailing spaces` #346	All checks have passed 2 successful checks continuous-integration/travis-ci/pr — The Travis CI build passed Details continuous-integration/travis-ci/push — The Travis CI build passed Details	`d71221c`
mothur-westcott	`Adjusts maximum quality score` #345	All checks have passed 2 successful checks continuous-integration/travis-ci/pr — The Travis CI build passed Details continuous-integration/travis-ci/push — The Travis CI build passed Details	`10cdcbc`
mothur-westcott	`Merge branch '1.40.0' into opti_improvements2`		`d25f5da`
mothur-westcott	`Creates SharedRabund class` SharedRabund allows for 0 otus in a sample, rabunds do not. SharedRabund also know their group. #347 #240		`83b5b56`
mothur-westcott	`Shared file data structure rewrite` #347 #240		`357b380`
mothur-westcott	`Fixes bugs while testing shared file rewrite` #357 #240 #347		`c0e36d6`
mothur-westcott	`WIP - testing shared file changes` #357 #347 #240		`4fbc5e1`
mothur-westcott	`Revert to previous`		`04c1c99`
mothur-westcott	`Fixes dot adjust for paired primers`		`524bf4a`
mothur-westcott	`Fixes while testing shared file change` #357 #347		`6c9959c`
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mothur-westcott	`Fixes chimera.vsearch screen output` #309	All checks have passed 2 successful checks continuous-integration/travis-ci/pr — The Travis CI build passed Details continuous-integration/travis-ci/push — The Travis CI build passed Details	`7b05930`
mothur-westcott	`Fixes current files saved by fastq.info` #339	All checks have passed 2 successful checks continuous-integration/travis-ci/pr — The Travis CI build passed Details continuous-integration/travis-ci/push — The Travis CI build passed Details	`fd928f0`

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1.40.0 #351

amirshams84 commented Jul 7, 2017

mothur-westcott added some commits Mar 27, 2017

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1.40.0 #351

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amirshams84 commented Jul 7, 2017

mothur-westcott added some commits Mar 27, 2017

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