[DO_NOT_MERGE] Rabbit Fix #14
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… with QS statistics for CB/UMI read.
…r to define minimum seed length.
… calculated only for CB/UMI portions of the read (alexdobin#798).
…ns are output even of reads do not match genes.
…eatures GeneFull only option alexdobin#902
…olo count matrix from the BAM output.
…g-faults for --runMode soloCellFiltering runs.
…hen only EM options is specified in --soloMultiMappers.
…ntain NH and AS tags for duplication removal jobs (--runMode inputAlignmentsFromBAM --bamRemoveDuplicatesType UniqueIdenticalNotMulti).
…ranscriptomeSAM output that resulted in both mapped and unmapped output for some reads. Many thanks to Diane Trout (@caltech) for helping to track this bug.
…Features Gene and GeneFull were used together with --soloCBmatchWLtype 1MM_multi_pseudocounts option.
…eFull_CR counting. The results show better agreement with CR --include-introns option.
… implement BAM output for multimappers.
…trFeature=featureFirst.
…st feature on the list is used for GX,GN,XB,UB tags.
…mes for both unique- and multi-gene reads. Note that GX/GN tags are used to output gene ID/name for unique-gene reads.
…ches and one insertion+deletion for --soloType CB_UMI_Complex.
…e CB_samTagOut and --soloCBwhitelist None are used together.
…age in case the *true empty* cells cannot be found.
…e offending read number and line.
…dFilesIn, check every file for access.
…hat resulted in a seg-fault whem mapping to the rabbit genome. Issue alexdobin#1223: fixed the N_unmapped value reported in ReadsPerGene.out.tab. The single-end (i.e. partially mapped alignment are not excluded from N_unmapped. dev_EoI_2.7.9a_2021-09-30
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Only here to see all the changes so I could verify that 10XGenomics/orbit@f87846f would solve this issue.