data/bcbio-1.2.4/HISTORY.md:44: explictly ==> explicitly data/bcbio-1.2.4/HISTORY.md:95: intial ==> initial data/bcbio-1.2.4/HISTORY.md:146: smoe ==> some data/bcbio-1.2.4/HISTORY.md:962: funtionality ==> functionality data/bcbio-1.2.4/HISTORY.md:973: compatbility ==> compatibility data/bcbio-1.2.4/HISTORY.md:992: explicity ==> explicitly data/bcbio-1.2.4/HISTORY.md:1028: corectly ==> correctly data/bcbio-1.2.4/bcbio/utils.py:338: fils ==> fills, files, file data/bcbio-1.2.4/bcbio/utils.py:345: fils ==> fills, files, file data/bcbio-1.2.4/bcbio/bam/fastq.py:47: thare ==> there data/bcbio-1.2.4/bcbio/chipseq/peaks.py:83: sucessfully ==> successfully data/bcbio-1.2.4/bcbio/distributed/objectstore.py:165: offests ==> offsets data/bcbio-1.2.4/bcbio/distributed/runfn.py:291: fuction ==> function data/bcbio-1.2.4/bcbio/distributed/transaction.py:106: extention ==> extension data/bcbio-1.2.4/bcbio/heterogeneity/bubbletree.py:1: freqencies ==> frequencies data/bcbio-1.2.4/bcbio/heterogeneity/bubbletree.py:63: paramters ==> parameters data/bcbio-1.2.4/bcbio/heterogeneity/loh.py:173: EDN ==> END data/bcbio-1.2.4/bcbio/ngsalign/bismark.py:125: disussion ==> discussion data/bcbio-1.2.4/bcbio/ngsalign/bwa.py:109: occurances ==> occurrences data/bcbio-1.2.4/bcbio/ngsalign/minimap2.py:31: inconsitent ==> inconsistent data/bcbio-1.2.4/bcbio/pipeline/disambiguate/run.py:166: stricly ==> strictly data/bcbio-1.2.4/bcbio/provenance/programs.py:215: Retreiving ==> Retrieving data/bcbio-1.2.4/bcbio/qc/kraken.py:60: comming ==> coming data/bcbio-1.2.4/bcbio/srna/mirdeep.py:35: instaled ==> installed data/bcbio-1.2.4/bcbio/srna/mirge.py:31: hsa ==> has data/bcbio-1.2.4/bcbio/structural/battenberg.py:41: caling ==> calling, scaling, culling data/bcbio-1.2.4/bcbio/structural/pindel.py:24: tupple ==> tuple data/bcbio-1.2.4/bcbio/structural/pindel.py:68: tupple ==> tuple data/bcbio-1.2.4/bcbio/structural/pindel.py:117: fro ==> for, from data/bcbio-1.2.4/bcbio/structural/pindel.py:118: tupple ==> tuple data/bcbio-1.2.4/bcbio/structural/regions.py:56: nin ==> inn, min, bin, nine data/bcbio-1.2.4/bcbio/structural/regions.py:200: creat ==> create data/bcbio-1.2.4/bcbio/structural/regions.py:359: caling ==> calling, scaling, culling data/bcbio-1.2.4/bcbio/structural/shared.py:296: Calcualtes ==> Calculates data/bcbio-1.2.4/bcbio/structural/titancna.py:66: cna ==> can data/bcbio-1.2.4/bcbio/structural/titancna.py:183: converstion ==> conversion, conversation data/bcbio-1.2.4/bcbio/upload/__init__.py:191: algorith ==> algorithm data/bcbio-1.2.4/bcbio/upload/irods.py:3: throught ==> thought, through, throughout data/bcbio-1.2.4/bcbio/variation/bedutils.py:21: alpha-numeric ==> alphanumeric data/bcbio-1.2.4/bcbio/variation/octopus.py:51: incompatibilies ==> incompatibilities data/bcbio-1.2.4/bcbio/variation/qsnp.py:97: tupples ==> tuples data/bcbio-1.2.4/bcbio/variation/samtools.py:26: metdata ==> metadata data/bcbio-1.2.4/bcbio/variation/scalpel.py:160: caling ==> calling, scaling, culling data/bcbio-1.2.4/bcbio/variation/validateplot.py:384: hist ==> heist, his data/bcbio-1.2.4/bcbio/wgbsseq/cpg_caller.py:126: chunck ==> chunk data/bcbio-1.2.4/bcbio/wgbsseq/cpg_caller.py:127: chunck ==> chunk data/bcbio-1.2.4/bcbio/wgbsseq/cpg_caller.py:128: chunck ==> chunk data/bcbio-1.2.4/bcbio/wgbsseq/cpg_caller.py:129: chunck ==> chunk data/bcbio-1.2.4/bcbio/wgbsseq/cpg_caller.py:130: chunck ==> chunk data/bcbio-1.2.4/bcbio/workflow/template.py:3: inpu ==> input data/bcbio-1.2.4/config/templates/freebayes-variant.yaml:14: targetted ==> targeted data/bcbio-1.2.4/config/templates/gatk-joint-genotyping.yaml:12: targetted ==> targeted data/bcbio-1.2.4/config/templates/gatk-variant.yaml:13: targetted ==> targeted data/bcbio-1.2.4/config/templates/illumina-srnaseq.yaml:12: hsa ==> has data/bcbio-1.2.4/config/templates/noalign-variant.yaml:17: targetted ==> targeted data/bcbio-1.2.4/config/templates/tumor-paired.yaml:19: targetted ==> targeted data/bcbio-1.2.4/docs/contents/atac.md:87: metdata ==> metadata data/bcbio-1.2.4/docs/contents/citations.md:25: arithmetics ==> arithmetic data/bcbio-1.2.4/docs/contents/citations.md:112: BA ==> BY, BE data/bcbio-1.2.4/docs/contents/cloud.md:77: keypair ==> key pair data/bcbio-1.2.4/docs/contents/configuration.md:253: pipeine ==> pipeline data/bcbio-1.2.4/docs/contents/configuration.md:541: hsa ==> has data/bcbio-1.2.4/docs/contents/development.md:52: commiting ==> committing data/bcbio-1.2.4/docs/contents/development.md:124: wihch ==> which data/bcbio-1.2.4/docs/contents/intro.md:74: contol ==> control data/bcbio-1.2.4/docs/contents/parallel.md:158: deamon ==> daemon data/bcbio-1.2.4/docs/contents/rnaseq_fusions.md:1: Detecing ==> Detecting data/bcbio-1.2.4/docs/contents/rnaseq_variants.md:164: discusion ==> discussion data/bcbio-1.2.4/docs/contents/single_cell.md:243: avaliable ==> available data/bcbio-1.2.4/docs/contents/small_rnaseq.md:31: hsa ==> has data/bcbio-1.2.4/docs/contents/structural_variants.md:44: Paramaters ==> Parameters data/bcbio-1.2.4/docs/contents/misc/bcbio-smallrna.bib:162: billon ==> billion data/bcbio-1.2.4/scripts/ansible/README.md:68: keypair ==> key pair data/bcbio-1.2.4/scripts/ansible/README.md:68: KeyPairs ==> key pairs data/bcbio-1.2.4/scripts/ansible/README.md:70: keypair ==> key pair data/bcbio-1.2.4/scripts/ansible/README.md:90: keypair ==> key pair data/bcbio-1.2.4/scripts/ansible/README.md:319: proceses ==> processes data/bcbio-1.2.4/scripts/ansible/launch_aws.yaml:19: keypair ==> key pair data/bcbio-1.2.4/scripts/ansible/launch_aws.yaml:19: keypair ==> key pair data/bcbio-1.2.4/tests/pytest.ini:48: functionaltiy ==> functionality data/bcbio-1.2.4/tests/data/automated/run_info-cwl.yaml:1: converstion ==> conversion, conversation data/bcbio-1.2.4/tests/data/automated/run_info-srnaseq_bowtie.yaml:12: hsa ==> has data/bcbio-1.2.4/tests/data/automated/run_info-srnaseq_star.yaml:12: hsa ==> has data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:864: AFE ==> SAFE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:5648: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:6140: EDE ==> EDGE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:9416: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:9576: IIF ==> IF data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:13388: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:15596: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:16136: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:17792: EGE ==> EDGE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:20808: DAA ==> DATA data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:24380: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:24512: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:26576: AFE ==> SAFE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:28332: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:31188: EDE ==> EDGE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:31712: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:36056: EDE ==> EDGE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:38696: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:39668: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:42732: EGE ==> EDGE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:43832: EDE ==> EDGE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:43832: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:43864: DED ==> DEAD data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:51916: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:57352: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:57424: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:67292: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:74612: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:77316: DED ==> DEAD data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:78272: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:80448: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:85844: DED ==> DEAD data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:91068: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:93504: EGE ==> EDGE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:94904: CACE ==> CACHE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:95548: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:96312: EGDE ==> EDGE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:96840: IIF ==> IF data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:102836: IIF ==> IF data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:119860: DAA ==> DATA data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:121616: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:121724: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca.fastq:121988: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:936: DAA ==> DATA data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:6080: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:6216: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:6652: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:10352: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:11248: EDE ==> EDGE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:16880: IIF ==> IF data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:18080: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:20104: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:25572: DED ==> DEAD data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:34000: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:34032: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:35520: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:36584: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:42620: EACF ==> EACH data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:53784: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:58860: EDE ==> EDGE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:65616: EGE ==> EDGE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:72464: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:73600: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:87488: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:89864: DED ==> DEAD data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:92356: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:95340: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:100496: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:105024: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:105876: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:106196: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:108960: EDE ==> EDGE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:110328: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:114272: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:122444: EDE ==> EDGE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:124772: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:128960: DAA ==> DATA data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:133472: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:135516: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:135616: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:135880: EGE ==> EDGE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:140640: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:140912: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_srnaseq/mirqca_2.fastq:140964: BA ==> BY, BE data/bcbio-1.2.4/tests/data/test_stranded/test_2.fq:128: ege ==> edge data/bcbio-1.2.4/tests/data/variants/S1-variants.vcf:8: sting ==> string data/bcbio-1.2.4/tests/data/variants/S1-variants.vcf:8: sting ==> string data/bcbio-1.2.4/tests/data/variants/S1-variants.vcf:8: sting ==> string data/bcbio-1.2.4/tests/data/variants/S1-variants.vcf:8: sting ==> string data/bcbio-1.2.4/tests/data/variants/S2-variants.vcf:8: sting ==> string data/bcbio-1.2.4/tests/data/variants/S2-variants.vcf:8: sting ==> string data/bcbio-1.2.4/tests/data/variants/S2-variants.vcf:8: sting ==> string data/bcbio-1.2.4/tests/data/variants/S2-variants.vcf:8: sting ==> string data/bcbio-1.2.4/debian/TODO:217: Addresss ==> Address data/bcbio-1.2.4/debian/changelog:139: incompatbility ==> incompatibility data/bcbio-1.2.4/debian/patches/spelling:11: Paramters ==> Parameters data/bcbio-1.2.4/debian/patches/spelling:22: commerical ==> commercial data/bcbio-1.2.4/debian/patches/spelling:31: commerical ==> commercial data/bcbio-1.2.4/debian/patches/spelling:42: occure ==> occur, occurred data/bcbio-1.2.4/debian/patches/spelling:53: ouput ==> output data/bcbio-1.2.4/debian/patches/spelling:64: ouput ==> output data/bcbio-1.2.4/debian/patches/spelling:75: commiting ==> committing data/bcbio-1.2.4/debian/patches/spelling:86: decribing ==> describing data/bcbio-1.2.4/.pc/do_not_use_git.patch/bcbio/provenance/programs.py:215: Retreiving ==> Retrieving