add optional stage1 methods to allow analysis using product crams as input (instead of default BCL)#331
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dozy wants to merge 9 commits into
Open
add optional stage1 methods to allow analysis using product crams as input (instead of default BCL)#331dozy wants to merge 9 commits into
dozy wants to merge 9 commits into
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add test for this
…te method; select between i2b or reanalysis from product crams using i2b_switch parameter, or select an arbitrary VTFILE template using the s1_produce_init_bam_method parameter incorporates required vtfp fix for parameter value inheritance bug
add --reject-PG flag to reset step
remove unneeded warn from test
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allow initial input bam to be produced by "bambi i2b" or some alternate method; select between i2b or reanalysis from product crams using i2b_switch parameter, or select an arbitrary VTFILE template using the s1_produce_init_bam_method parameter
incorporates required vtfp fix for parameter value inheritance bug