diff --git a/enclone_args/src/load_gex.rs b/enclone_args/src/load_gex.rs index b1ad8ef13..14ebd372f 100644 --- a/enclone_args/src/load_gex.rs +++ b/enclone_args/src/load_gex.rs @@ -19,11 +19,6 @@ use vector_utils::{bin_position, unique_sort}; pub fn get_gex_info(ctl: &mut EncloneControl) -> Result { let mut gex_features = Vec::>::new(); let mut gex_barcodes = Vec::>::new(); - let mut fb_total_umis = Vec::::new(); - let mut fb_total_reads = Vec::::new(); - let mut fb_brn = Vec::>::new(); - let mut fb_brnr = Vec::>::new(); - let mut fb_bdcs = Vec::>::new(); let mut feature_refs = Vec::::new(); let mut cluster = Vec::>::new(); let mut cell_type = Vec::>::new(); @@ -42,11 +37,6 @@ pub fn get_gex_info(ctl: &mut EncloneControl) -> Result { ctl, &mut gex_features, &mut gex_barcodes, - &mut fb_total_umis, - &mut fb_total_reads, - &mut fb_brn, - &mut fb_brnr, - &mut fb_bdcs, &mut feature_refs, &mut cluster, &mut cell_type, @@ -86,29 +76,26 @@ pub fn get_gex_info(ctl: &mut EncloneControl) -> Result { let mut h5_data = Vec::>::new(); let mut h5_indices = Vec::>::new(); let mut h5_indptr = Vec::>::new(); - if ctl.gen_opt.h5 { - let gex_outs = &ctl.origin_info.gex_path; - for i in 0..ctl.origin_info.dataset_path.len() { - // let bin_file = format!("{}/feature_barcode_matrix.bin", gex_outs[i]); - if !gex_outs[i].is_empty() - /* && !(path_exists(&bin_file) && !ctl.gen_opt.force_h5) */ - { - let f = &h5_paths[i]; - let h = hdf5::File::open(f).unwrap(); + let gex_outs = &ctl.origin_info.gex_path; + for i in 0..ctl.origin_info.dataset_path.len() { + if !gex_outs[i].is_empty() { + let f = &h5_paths[i]; - h5_data.push(Some(h.dataset("matrix/data").unwrap())); - h5_indices.push(Some(h.dataset("matrix/indices").unwrap())); - let indptr = h.dataset("matrix/indptr").unwrap(); - let x: Vec = indptr.as_reader().read().unwrap().to_vec(); - h5_indptr.push(x); - } else { - h5_data.push(None); - h5_indices.push(None); - h5_indptr.push(Vec::::new()); - } + let h = hdf5::File::open(f).unwrap(); + + h5_data.push(Some(h.dataset("matrix/data").unwrap())); + h5_indices.push(Some(h.dataset("matrix/indices").unwrap())); + let indptr = h.dataset("matrix/indptr").unwrap(); + let x: Vec = indptr.as_reader().read().unwrap().to_vec(); + h5_indptr.push(x); + } else { + h5_data.push(None); + h5_indices.push(None); + h5_indptr.push(Vec::::new()); } } + fn compute_feature_id(gex_features: &[String]) -> HashMap { let mut x = HashMap::::new(); for (j, f) in gex_features.iter().enumerate() { @@ -152,11 +139,6 @@ pub fn get_gex_info(ctl: &mut EncloneControl) -> Result { Ok(GexInfo { gex_features, gex_barcodes, - fb_total_umis, - fb_total_reads, - fb_brn, - fb_brnr, - fb_bdcs, feature_refs, cluster, cell_type, diff --git a/enclone_args/src/load_gex_core.rs b/enclone_args/src/load_gex_core.rs index fca062e05..f0b3b097e 100644 --- a/enclone_args/src/load_gex_core.rs +++ b/enclone_args/src/load_gex_core.rs @@ -13,14 +13,7 @@ use io_utils::{dir_list, open_for_read, open_userfile_for_read, path_exists}; use itertools::Itertools; use rayon::prelude::*; use serde_json::Value; -use std::{ - collections::HashMap, - convert::TryInto, - fmt::Write, - fs::read_to_string, - io::{BufRead, Read}, - time::Instant, -}; +use std::{collections::HashMap, fmt::Write, fs::read_to_string, io::BufRead, time::Instant}; use string_utils::{parse_csv, TextUtils}; use vector_utils::{unique_sort, VecUtils}; @@ -41,23 +34,13 @@ struct LoadResult { feature_metrics: HashMap<(String, String), String>, json_metrics: HashMap, metrics: String, - fb_total_umis: u64, - fb_brn: Vec<(String, u32, u32)>, feature_refs: String, - fb_brnr: Vec<(String, u32, u32)>, - fb_total_reads: u64, - fb_bdcs: Vec<(String, u32, u32, u32)>, } pub fn load_gex( ctl: &mut EncloneControl, gex_features: &mut Vec>, gex_barcodes: &mut Vec>, - fb_total_umis: &mut Vec, - fb_total_reads: &mut Vec, - fb_brn: &mut Vec>, - fb_brnr: &mut Vec>, - fb_bdcs: &mut Vec>, feature_refs: &mut Vec, cluster: &mut Vec>, cell_type: &mut Vec>, @@ -548,80 +531,6 @@ pub fn load_gex( r.gex_mult = gene_mult; r.fb_mult = fb_mult; - // Read the total UMIs. - - let top_file = fnx(&outs, "feature_barcode_matrix_top.total"); - if path_exists(&top_file) { - pathlist.push(top_file.clone()); - let mut f = open_for_read![&top_file]; - let mut bytes = Vec::::new(); - f.read_to_end(&mut bytes).unwrap(); - r.fb_total_umis = u64::from_ne_bytes(bytes.try_into().unwrap()); - } - - // Read the total reads. - - let top_file = fnx(&outs, "feature_barcode_matrix_top.total_reads"); - if path_exists(&top_file) { - pathlist.push(top_file.clone()); - let mut f = open_for_read![&top_file]; - let mut bytes = Vec::::new(); - f.read_to_end(&mut bytes).unwrap(); - r.fb_total_reads = u64::from_ne_bytes(bytes.try_into().unwrap()); - } - - // Read the barcode-ref-nonref UMI count file. - - let brn_file = fnx(&outs, "feature_barcode_matrix_top.brn"); - if path_exists(&brn_file) { - pathlist.push(brn_file.clone()); - let f = open_for_read![&brn_file]; - for line in f.lines() { - let s = line.unwrap(); - let fields = parse_csv(&s); - r.fb_brn.push(( - fields[0].to_string(), - fields[1].parse::().unwrap(), - fields[2].parse::().unwrap(), - )); - } - } - - // Read the barcode-ref-nonref read count file. - - let brnr_file = fnx(&outs, "feature_barcode_matrix_top.brnr"); - if path_exists(&brnr_file) { - pathlist.push(brnr_file.clone()); - let f = open_for_read![&brnr_file]; - for line in f.lines() { - let s = line.unwrap(); - let fields = parse_csv(&s); - r.fb_brnr.push(( - fields[0].to_string(), - fields[1].parse::().unwrap(), - fields[2].parse::().unwrap(), - )); - } - } - - // Read the bdcs read count file. - - let bdcs_file = fnx(&outs, "feature_barcode_matrix_top.bdcs"); - if path_exists(&bdcs_file) { - pathlist.push(bdcs_file.clone()); - let f = open_for_read![&bdcs_file]; - for line in f.lines() { - let s = line.unwrap(); - let fields = parse_csv(&s); - r.fb_bdcs.push(( - fields[0].to_string(), - fields[1].parse::().unwrap(), - fields[2].parse::().unwrap(), - fields[3].parse::().unwrap(), - )); - } - } - // Read the feature reference file. let fref_file = fnx(&outs, "feature_reference.csv"); @@ -717,12 +626,7 @@ pub fn load_gex( feature_metrics.push(r.feature_metrics); json_metrics.push(r.json_metrics); metrics.push(r.metrics); - fb_total_umis.push(r.fb_total_umis); - fb_brn.push(r.fb_brn); feature_refs.push(r.feature_refs); - fb_brnr.push(r.fb_brnr); - fb_total_reads.push(r.fb_total_reads); - fb_bdcs.push(r.fb_bdcs); } // Done. diff --git a/enclone_core/src/defs.rs b/enclone_core/src/defs.rs index 6cc3452f5..a5e7e011f 100644 --- a/enclone_core/src/defs.rs +++ b/enclone_core/src/defs.rs @@ -135,7 +135,6 @@ pub struct GeneralOpt { pub fate_file: String, // Optional path to a json file containing metadata pub proto_metadata: Option, - pub h5: bool, pub h5_pre: bool, pub accept_reuse: bool, pub descrip: bool, @@ -823,11 +822,6 @@ pub struct CloneInfo { pub struct GexInfo { pub gex_features: Vec>, pub gex_barcodes: Vec>, - pub fb_total_umis: Vec, - pub fb_total_reads: Vec, - pub fb_brn: Vec>, - pub fb_brnr: Vec>, - pub fb_bdcs: Vec>, pub feature_refs: Vec, pub gex_cell_barcodes: Vec>, pub cluster: Vec>, diff --git a/enclone_core/src/lib.rs b/enclone_core/src/lib.rs index 4a55b599a..eae185b2c 100644 --- a/enclone_core/src/lib.rs +++ b/enclone_core/src/lib.rs @@ -11,7 +11,6 @@ pub mod hcomp; pub mod join_one; pub mod linear_condition; pub mod logging; -pub mod main_testlist; pub mod mammalian_fixed_len; pub mod median; pub mod opt_d; diff --git a/enclone_core/src/main_testlist.rs b/enclone_core/src/main_testlist.rs deleted file mode 100644 index f3066c5aa..000000000 --- a/enclone_core/src/main_testlist.rs +++ /dev/null @@ -1,766 +0,0 @@ -// Copyright (c) 2021 10X Genomics, Inc. All rights reserved. - -pub const TESTS: [&str; 305] = [ - // 1. tests variant base after CDR3, parseable output - r###"BCR=123089 CDR3=CVRDRQYYFDYW POUT=stdout - PCOLS=exact_subclonotype_id,n,v_name1,v_name2,nchains,var_indices_aa1,barcodes"###, - // 2. tests many donor ref differences, test comp, edit and var and donorn - r###"BCR=123089 CDR3=CARRYFGVVADAFDIW CVARSP=comp,edit,var AMINO=cdr3,var,share,donorn"###, - // 3. tests motif in CDR3, CHAINS, u_sum, ulen, flipped args in CVARS, on tiny dataset - r###"BCR=85333 CDR3="CAA.*" CHAINS=2 CVARS=const,u_sum,ulen"###, - // 4. tests gex and antibody, FULL_SEQC, ulen, udiff, on tiny dataset - r###"BCR=86237 GEX=85679 LVARSP=gex,CD19_ab_μ,CD25_ab_μ,IGLV3-1_g_μ,IGLV3-1_g_%,RPS27_g_μ - CELLS=3 FULL_SEQC SUM MEAN - CVARSP=ulen,udiff"###, - // 5. tests TCR and correct grouping of onesies on AGBT Donor 2 dataset - r###"TCR=101287 MIN_CELLS=100"###, - // 6. tests AMINO= and vjlen and other things - r###"BCR=86237 CELLS=3 AMINO= CVARS=u,r,cdr3_dna,cdr3_len,vjlen"###, - // 7. tests SHM deletion - r###"BCR=123085 CVARSP=var,clen,cdiff CDR3=CAREPLYYDFWSAYFDYW LVARSP=near,far"###, - // 8. test KEEP_CELL_IF with >= and <= - r###"BCR=123085 BC=testx/inputs/123077_cells.csv PER_CELL LVARSP=rank - KEEP_CELL_IF="rank >= 2 && rank <= 3""###, - // 9. tests PER_CELL and unicode - r###"BCR=█≈ΠΠΠ≈█ CDR3=CAKGDRTGYSYGGGIFDYW PER_CELL"###, - // 10. tests multiple datasets and also LVARS=n,origins,donors,datasets, and share - // Note that we have deliberately "faked" two donors. In reality there is one. - r###"BCR="123085;123089" CDR3=CVKDRVTGTITELDYW LVARS=n,origins,donors,datasets AMINO=share - MIX_DONORS"###, - // 11. tests META, and CONST_IGH + META, which was broken at one point - r###"META=testx/inputs/test11_meta CDR3=CARSFFGDTAMVMFQAFDPW LVARSP=donors,gex - CONST_IGH=IGHD"###, - // 12. test colon lvar in KEEP_CLONO_IF_CELL_MEAN= and test for parsing error at + - r###"BCR=86237 GEX=85679 LVARSP=g37:IGHV3-7_g_μ KEEP_CLONO_IF_CELL_MEAN="n + g37 >= 5.5" - MIN_CHAINS=2 NH5"###, - // 13. check TSV file with BC - r###"BCR=123085 BC=testx/inputs/123077_cells.tsv PER_CELL LVARSP=T CDR3=CARGYEDFTMKYGMDVW"###, - // 14. test cdr3_aa_conp - r###"BCR=123085 CVARSP=cdr3_aa_conp CDR3=CAKTGDLELRYFDWDMDVW"###, - // 15. tests insertion and AMINO range; also this incorrectly reported an insertion before - // it was fixed - r###"BCR=86233 CDR3=CARGLVVVYAIFDYW CVARS=notes AMINO=cdr3,105-113"###, - // 16. tests number of cells broken out by dataset - r###"BCR=123085,123089 LVARS=n,n_123085,n_123089 CDR3=CTRDRDLRGATDAFDIW"###, - // 17. tests gex with PER_CELL and tests n_gex - // See also enclone_test_prebuild below, that tests nearly the same thing, - // and tests versus the same output file. - r###"BCR=86237 GEX=85679 LVARSP=gex_max,gex,n_gex,CD19_ab_μ CELLS=3 PER_CELL NH5"###, - // 18. makes sure cross filtering isn't applied to two origins from same donor - r###"BCR=123085:123089 CDR3=CVRDEGGARPNKWNYEGAFDIW"###, - // 19. there was a bug that caused a twosie to be deleted, and there was foursie junk - // There were also some cells that were lost due to a bug in graph filtering. - r###"BCR=123085 CDR3=CARRYFGVVADAFDIW"###, - // 20. example affected by whitelist (gel bead oligo contamination) filtering, and test u_Σ - r###"BCR=52177 AMINO=cdr3 PER_CELL CDR3=CATWDDSLSGPNWVF CVARSP=u_Σ"###, - // 21. test MIN_CHAINS_EXACT - r###"BCR=123089 CDR3=CGTWHSNSKPNWVF MIN_CHAINS_EXACT=3"###, - // 22. DUPLICATE, TO REMOVE - r###"BCR=123089 CDR3=CGTWHSNSKPNWVF MIN_CHAINS_EXACT=3"###, - // 23. here we were generating a fake alternate allele - r###"BCR=83808 CDR3=CAREGRGMVTTNPFDYW MIN_CELLS_EXACT=30"###, - // 24. an example that uses IGHE, and test NGROUP - r###"BCR=52177 CDR3=CSTGWGLDFDFWSGYYTAGYHW NGROUP"###, - // 25. add mouse B6 example that had messed up constant regions - r###"TCR=74396 MOUSE CVARSP=cdiff CDR3=CASSDAGDTQYF"###, - // 26. tests multiple datasets and also LVARS=n,donors,datasets, and share - // Note that we have deliberately "faked" two donors. In reality there is one. - // Here we make sure that non-specification of MIX_DONORS works. - r###"BCR="123085;123089" CDR3=CVKDRVTGTITELDYW"###, - // 27. tests SUMMARY and NOPRINT - r###"BCR=123085 SUMMARY SUMMARY_CLEAN NOPRINT"###, - // 28. tests BARCODE option - r###"BCR=165807 BARCODE=CCCATACGTGATGATA-1,TCTATTGAGCTGAAAT-1"###, - // 29. tests KEEP_CLONO_IF_CELL_MAX and parenthesized variable in it, SUM and MEAN, use of ≥ - r###"BCR=123085 GEX=123217 LVARSP=IGHV3-7_g,IGHV3-7_g_μ - KEEP_CLONO_IF_CELL_MAX="(IGHV3-7_g_μ)≥10000.0" MIN_CHAINS=2 SUM MEAN H5"###, - // 30. tests d_univ and d_donor - r###"BCR=123085 CVARSP=d_univ,d_donor CDR3=CVKDRVTGTITELDYW"###, - // 31. tests Cell Ranger 3.1 output - r###"BCR=../3.1/123085 CDR3=CVKDRVTGTITELDYW ACCEPT_BROKEN"###, - // 32. tests Cell Ranger 2.0 output and RE - r###"BCR=../2.0/124550 CDR3=CAREPLYYDFWSAYFDYW RE ACCEPT_BROKEN"###, - // 33. tests SCAN - r###"BCR=123085 GEX=123217 LVARSP=IGHV1-69D_g_μ MIN_CELLS=10 NGEX - SCAN="(IGHV1-69D_g_μ)>=100,(IGHV1-69D_g_μ)<=1,t-10*c>=0.1" NOPRINT H5"###, - // 34. tests honeycomb plot - // (This yields a lot of output so will be annoying to debug if something changes.) - r###"BCR=123085:123089 MIN_CELLS=10 PLOT="stdout,s1->red,s2->blue" NOPRINT - LEGEND=red,"cell from 123085",blue,"cell from 123089""###, - // 35. tests barcode-by-barcode specification of colors, and tests LEGEND= - // Note that the specification of PRE overrides our usual specification. - // (This yields a lot of output so will be annoying to debug if something changes.) - r###"PRE=../enclone-data/big_inputs/version{TEST_FILES_VERSION},. - META=testx/inputs/test35_meta MIN_CELLS=10 MIN_CHAINS_EXACT=2 NOPRINT PLOT=stdout NO_PRE - LEGEND=red,IGHG1,green,IGHG3,blue,IGHA1,orange,IGHM,black,unassigned"###, - // 36. tests PCELL and u_Σ in PCOLS (both forms) - r###"BCR=85333 CDR3=CARDGMTTVTTTAYYGMDVW POUT=stdout PCELL CVARSP=u_Σ - PCOLS=barcode,const1,const2,u_Σ1,u_sum1"###, - // 37. tests parseable output of barcodes for a given dataset - r###"BCR=123085,123089 POUT=stdout PCOLS=123085_barcodes,123089_barcodes - CDR3=CAVTIFGVRTALPYYYALDVW"###, - // 38. tests parseable output of barcodes for a given dataset, using PCELL - r###"BCR=123085,123089 POUT=stdout PCOLS=123085_barcode,123089_barcode PCELL - CDR3=CAVTIFGVRTALPYYYALDVW"###, - // 39. tests u and r fields in parseable output, and tests stdouth - r###"BCR=85333 POUT=stdouth PCOLS=barcode,u1,u_cell1,r2,r_cell2 PCELL PER_CELL CVARSP=r - CDR3=CAADGGGDQYYYMDVW"###, - // 40. indel was wrong - // Note that F is deprecated, equals KEEP_CLONO_IF_CELL_MEAN. Also test ⩾. - r###"BCR=86237 GEX=85679 LVARSP=IGHV3-7_g_μ F="(IGHV3-7_g_μ)⩾4.5" MIN_CHAINS=2 SUM MEAN - NH5"###, - // 41. test case for gex_cell - r###"BCR=86237 GEX=85679 CDR3=CAKAVAGKAVAGGWDYW POUT=stdouth PCOLS=gex_cell PCELL NH5"###, - // 42. test case that should fail because gex_cell doesn't make sense without gex data - r###"BCR=85333 CDR3=CQQRSNWPLYTF POUT=stdouth PCOLS=gex_cell PCELL PER_CELL EXPECT_FAIL"###, - // 43. test case that should fail because _cell variables can't be used in LVARS - r###"BCR=86237 GEX=85679 CDR3=CAKAVAGKAVAGGWDYW LVARS=gex_cell EXPECT_FAIL"###, - // 44. test _cell - r###"BCR=86237 GEX=85679 LVARSP=gex,RPS27_g_μ CELLS=3 POUT=stdouth - PCOLS=barcode,gex_cell,CD19_ab,CD19_ab_cell NH5 PCELL"###, - // 45. test ndiff... - r###"BCR=123085 CVARSP=ndiff1vj,ndiff2vj CDR3=CARDQNFDESSGYDAFDIW"###, - // 46. test u_μ, u_min, r_μ, r_min and r_max - r###"BCR=85333 CVARSP=u_μ,u_min,u_max,r,r_μ,r_min,r_max AMINO=cdr3 CDR3=CAADGGGDQYYYMDVW - POUT=stdouth PCOLS=u_μ1,u_min1,u_max1,r2,r_μ2,r_min2,r_max2"###, - // 47. this should fail - r###"BCR=85333 CDR3=CAREEYYYDSSGDAFDIW LVARSP=gex_mean EXPECT_FAIL"###, - // 48. test gex_mean and gex_Σ and NGEX - // Do not use NH5 because the bin file is too big for git. - r###"BCR=123085 GEX=123217 LVARSP=gex_mean,gex_Σ CDR3=CASRKSGNYIIYW NGEX H5"###, - // 49. test HTML - r###"BCR=85333 CDR3=CAAWDDSLNGWVF CHAINS=1 POUT=stdouth PCOLS=barcodes,n FASTA=stdout - FASTA_AA=stdout HTML=CAAWDDSLNGWVF"###, - // 50. make sure this doesn't fail - r###"NOPAGER EXPECT_OK"###, - // 51. make sure this fails gracefully - r###"BCR=123085 PLOT=/nonexistent/broken.svg NOPRINT MIN_CELLS=50 EXPECT_FAIL"###, - // 52. add test for some gene patterns - // Do not use NH5 because the bin file is too big for git. - r###"BCR=123085 GEX=123217 CDR3=CARPKSDYIIDAFDIW MIN_CELLS=10 H5 - LVARSP="(IGHV5-51|IGLV1-47)_g_%,IGH.*_g_%,IG(K|L).*_g_%""###, - // 53. add test for _% with PER_CELL - // Do not use NH5 because the bin file is too big for git. - r###"BCR=123085 GEX=123217 LVARSP="gex,n_gex,JCHAIN_g_%,IG%:IG.*_g_%" CVARS=u_μ,const - MIN_CHAINS_EXACT=2 CDR3=CAREGGVGVVTATDWYFDLW PER_CELL H5"###, - // 54. make sure this fails gracefully - r###"BCR=86237 GEX=85679 LVARSP=GERBULXXX123_g_% EXPECT_FAIL"###, - // 55. test cred - r###"BCR=86237 GEX=85679 LVARSP=cred PCELL PER_CELL POUT=stdouth PCOLS=cred_cell - CDR3=CARSFFGDTAMVMFQAFDPW"###, - // 56. test SVG - r###"BCR=85333 CDR3=CARDPRGWGVELLYYMDVW SVG NGROUP"###, - // 57. test 1/8 for newline correctness - r###"BCR=85333 CDR3="CLLSYSGARVF|CQSADSSGTYKVF" AMINO= PLAIN SET_IN_STONE"###, - // 58. test 2/8 for newline correctness - r###"BCR=85333 CDR3="CLLSYSGARVF|CQSADSSGTYKVF" AMINO= PLAIN NGROUP SET_IN_STONE"###, - // 59. test 3/8 for newline correctness - r###"BCR=85333 CDR3="CLLSYSGARVF|CQSADSSGTYKVF" AMINO= PLAIN HTML SET_IN_STONE"###, - // 60. test 4/8 for newline correctness - r###"BCR=85333 CDR3="CLLSYSGARVF|CQSADSSGTYKVF" AMINO= PLAIN NGROUP HTML SET_IN_STONE"###, - // 61. test that enclone doesn't crash on CS multi 6.1 pipeline - r###"BCR_GEX=tiny_multi_CS_6.1 ALLOW_INCONSISTENT EXPECT_OK"###, - // 62. make sure color from BC can be used as lead variable was broken) - r###"BCR=123085 BC=testx/inputs/123077_cells.csv PER_CELL LVARSP=color - AMINO=cdr3 BARCODE=CATATGGTCAGTTGAC-1"###, - // 63. DUPLICATE, TO REPLACE - r###"BCR=85333 GROUP_VJ_REFNAME MIN_GROUP=2 AMINO= PLAIN HTML SET_IN_STONE"###, - // 64. DUPLICATE, TO REPLACE - r###"BCR=85333 GROUP_VJ_REFNAME MIN_GROUP=2 AMINO= PLAIN HTML NGROUP SET_IN_STONE"###, - // 65. test NCELL - r###"BCR=86237 NCELL CDR3=CAKTATTLGGYYSHGLDVW MIN_CELLS=2"###, - // 66. test BC in combination with PER_CELL and PCELL - // Do not use NH5 because the bin file is too big for git. - r###"BCR=123085 GEX=123217 BC=testx/inputs/123077_cells.csv PER_CELL LVARSP=gex,cred,T PCELL - POUT=stdouth PCOLS=barcode,T CDR3=CAKAGPTESGYYVWYFDLW MIN_CELLS=2 H5"###, - // 67. expect fail if garbage PRE - r###"PRE=garbage_gerbil_stuff BCR=86237 CELLS=3 EXPECT_FAIL NO_PRE"###, - // 68. a test of PRE - r###"PRE=mumbo_jumbo,../enclone-data/big_inputs/version{TEST_FILES_VERSION} BCR=86237 NO_PRE - CDR3=CARENHPVEYCSSTSCYKAYYYGMDVW"###, - // 69. another test of pre - r###"PRE=mumbo_jumbo BCR=../enclone-data/big_inputs/version{TEST_FILES_VERSION}/86237 NO_PRE - CDR3=CARENHPVEYCSSTSCYKAYYYGMDVW"###, - // 70. another test of META - r###"META=mumbo_jumbo EXPECT_FAIL"###, - // 71. another test of META - r###"PRE=../enclone-data/big_inputs/version{TEST_FILES_VERSION},testx/inputs META=test11_meta - CDR3=CARSFFGDTAMVMFQAFDPW LVARSP=donors,gex NO_PRE"###, - // 72. test SUMMARY_CSV - r###"BCR=86237 NOPRINT SUMMARY_CSV"###, - // 73. test cdr3_aa_conx - r###"BCR=123085 CVARSP=cdr3_aa_conx CDR3=CAKTGDLELRYFDWDMDVW"###, - // 74. this changed after a bug was fixed; the RE can probably be dropped later when we - // rerun all the datasets - r###"BCR=123085 RE CDR3=CARGYEDFTMKYGMDVW POUT=stdouth PCOLS=utr_id2"###, - // 75. this changed after a bug in RE was fixed, and this is in fact testing RE - r###"BCR=123085 CDR3=CQQSYSTPRTF RE"###, - // 76. test PLOT_BY_ISOTYPE - r###"BCR=123085 MIN_CELLS=10 PLOT_BY_ISOTYPE=stdout NOPRINT MIN_CHAINS_EXACT=2"###, - // 77. test PLOT_BY_ISOTYPE_COLOR - r###"BCR=123085 MIN_CELLS=10 PLOT_BY_ISOTYPE=stdout NOPRINT MIN_CHAINS_EXACT=2 - PLOT_BY_ISOTYPE_COLOR=red,green,blue,yellow,black,orange,turquoise,pink,gray,purple"###, - // 78. make sure that POUT with PCELL works on full dataset - r###"BCR=86237 POUT=stdout PCELL EXPECT_OK"###, - // 79. make sure that POUT works on full dataset with gex - r###"BCR=86237 GEX=85679 POUT=stdout NGEX NCELL EXPECT_OK"###, - // 80. make sure that POUT with PCELL works on full dataset with gex - r###"BCR=86237 GEX=85679 POUT=stdout PCELL NGEX NCELL EXPECT_OK"###, - // 81. IG:IG.*_g_%_cell and variants in parseable output - r###"BCR=86237 GEX=85679 CDR3=CARSFFGDTAMVMFQAFDPW POUT=stdouth PCELL - PCOLS="barcode,IG:IG.*_g_%_cell,IG.*_g_%_cell,IGN:IG.*_g_%,IG.*_g_%""###, - // 82. test entropy - // Do not use NH5 because the bin file is too big for git. - r###"BCR=123085 GEX=123217 LVARSP=entropy PER_CELL POUT=stdouth PCELL - PCOLS=barcode,entropy,entropy_cell CDR3=CARAQRHDFWGGYYHYGMDVW H5"###, - // 83. test COMPLETE and dref - r###"BCR=86237 CDR3=CARSFFGDTAMVMFQAFDPW COMPLETE LVARSP=dref"###, - // 84. test CLUSTAL_AA - r###"BCR=123085 CDR3=CAADRQLWSRSPGDYIYYGMQVW CLUSTAL_AA=stdout"###, - // 85. test NALL - r###"BCR=86237 NALL CDR3=CARAPEDTSRWPQYNYSGLDVW SEG=IGKV3-15"###, - // 86. test CLUSTAL_DNA - r###"BCR=86237 CDR3=CARSFFGDTAMVMFQAFDPW CLUSTAL_DNA=stdout"###, - // 87. test PHYLIP_AA and COLOR=codon - r###"BCR=123085 CDR3=CAADRQLWSRSPGDYIYYGMQVW PHYLIP_AA=stdout COLOR=codon"###, - // 88. test PHYLIP_DNA and COLOR=default - r###"BCR=123085 CDR3=CAADRQLWSRSPGDYIYYGMQVW PHYLIP_DNA=stdout COLOR=property"###, - // 89. test TREE and NEWICK - r###"BCR=123085 COMPLETE TREE NEWICK CDR3=CARDLGGRYYGSKDPW"###, - // 90. test KEEP_CELL_IF with non-null value - // Do not use NH5 because the bin file is too big for git. - r###"BCR=123085 GEX=123217 H5 BC=testx/inputs/123077_cells.csv PER_CELL LVARSP=gex,cred,T - CDR3=CARGYEDFTMKYGMDVW KEEP_CELL_IF="keeper == 'yes'""###, - // 91. test FCELL with null value - // Do not use NH5 because the bin file is too big for git. - r###"BCR=123085 GEX=123217 H5 BC=testx/inputs/123077_cells.csv PER_CELL LVARSP=gex,cred,T - CDR3=CARGYEDFTMKYGMDVW FCELL="keeper == ''""###, - // 92. test NALL_CELL - r###"BCR=123085 NALL_CELL CDR3=CQKYDSAPLTF MIN_CELLS=20"###, - // 93. test MIN_DATASET_RATIO - r###"BCR=123085,123089 MIN_DATASET_RATIO=6 LVARSP=nd2"###, - // 94. test use of SEG twice - r###"BCR=123085 SEG=IGHV5-51 SEG=IGKV1D-39"###, - // 95. test TREE=const - r###"BCR=123085 TREE=const CDR3=CARPKSDYIIDAFDIW MIN_CELLS=2"###, - // 96. test MAX_LOG_SCORE - r###"BCR=123085 CDR3=CARDQNFDESSGYDAFDIW MAX_LOG_SCORE=0.0"###, - // 97. Test MAX_CDR3_DIFFS. This is also an instance where an exact subclonotype has - // two chains with indentical CDR3s, and this is the right answer, until and unless we change - // cellranger to somehow not emit two such chains. - r###"BCR=123085 CDR3=CARESVVGLLPIFDYW MAX_CDR3_DIFFS=1"###, - // 98. test reduced stringency D alignment - // (RE can be removed once cellranger rerun) - r###"TCR=101287 CDR3=CASSPAGTSGKVWGTDTQYF RE"###, - // 99. test mait (redundant with mait_example.html below, so could delete) - r###"TCR=101287 LVARSP=mait CDR3=CSAGQGDTEAFF"###, - // 100. test inkt and INKT - r###"TCR=101287 LVARSP=inkt INKT MIN_CELLS=2"###, - // 101. test MAIT - r###"TCR=101287 LVARSP=mait MAIT MIN_CELLS=50"###, - // 102. test BINARY with unwriteable path - r###"BCR=123085 BINARY=/gerbilspam/bumblebee EXPECT_FAIL"###, - // 103. test POUT without PCOLS (somewhat annoying, because easily triggered to change) - r###"BCR=85333 POUT=stdout CDR3=CQSADSSGTYKVF"###, - // 104. test EASY - r###"BCR=123085 CDR3="CARVIVGPKKLEGRLYSSSLHFDCW|CARVIVGPEKQEGRLYSSSLHFDYW" EASY - MAX_LOG_SCORE=100"###, - // 105. test MAX_DEGRADATION and MAX_DIFFS - r###"BCR=123085,123089 MAX_LOG_SCORE=100 MAX_DEGRADATION=150 MAX_DIFFS=200 - MAX_CDR3_DIFFS=100 CDR3=CVRILGRALTVRVYFYYGIDVW"###, - // 106. test for failed interaction between POUT and COMPLETE (crashed at one point) - r###"BCR=123085 CDR3=CAKANQLLYGGRQYYYGMDVW COMPLETE POUT=stdout - PCOLS=clonotype_id,exact_subclonotype_id,n,d_donor1,d_donor2"###, - // 107. part 1 of test for weak onesies filter - r###"TCR=101287 CDR3=CASSQVAGAGQPQHF"###, - // 108. part 2 of test for weak onesies filter - r###"TCR=101287 CDR3=CASSQVAGAGQPQHF NWEAK_ONESIES"###, - // 109. test Levenshtein distance pattern - r###"BCR=123085 CDR3="CAKDKVPRRSSWSVFDYYGMDVW~9|CAVTIFGVRTALPYYYALDVW~9" NGROUP"###, - // 110. test dref_aa - r###"BCR=123085 LVARSP=dref,dref_aa CDR3=CAREKGIGSSGWDWGAFDIW"###, - // 111. test for fail if F used with unsupported variable (but now supported) - // Note that F is deprecated, equals KEEP_CLONO_IF_CELL_MEAN. - r###"BCR=123085 LVARSP=near F="near>=0" EXPECT_OK"###, - // 112. test 1 of 6 for cdr1/cdr2 in AMINO - r###"BCR=85333 CDR3=CARDLRVEGFDYW AMINO=var,share,donor,cdr1,cdr2,cdr3"###, - // 113. test 2 of 6 for cdr1/cdr2 in AMINO - r###"BCR=85333 CDR3=CARDLRVEGFDYW AMINO=var,share,donor,cdr1,cdr3"###, - // 114. test 3 of 6 for cdr1/cdr2 in AMINO - r###"BCR=85333 CDR3=CARDLRVEGFDYW AMINO=var,share,donor,cdr2,cdr3"###, - // 115. test 4 of 6 for cdr1/cdr2 in AMINO - r###"BCR=85333 CDR3=CARDLRVEGFDYW AMINO=var,share,donor,cdr1,cdr2"###, - // 116. test 5 of 6 for cdr1/cdr2 in AMINO - r###"BCR=85333 CDR3=CARDLRVEGFDYW AMINO=var,share,donor,cdr1"###, - // 117. test 6 of 6 for cdr1/cdr2 in AMINO - r###"BCR=85333 CDR3=CARDLRVEGFDYW AMINO=var,share,donor,cdr2"###, - // 118. test cdr1_aa and cdr2_aa - r###"BCR=85333 CDR3=CARDLRVEGFDYW CVARSP=cdr1_aa,cdr2_aa AMINO=cdr1"###, - // 119. test cdr3_aa - r###"BCR=85333 CDR3=CARDLRVEGFDYW CVARSP=cdr3_aa AMINO=cdr3"###, - // 120. test cdr1_dna and cdr2_dna - r###"BCR=85333 CDR3=CARDLRVEGFDYW CVARS=cdr1_dna,cdr2_dna AMINO="###, - // 121. test cdr1_len and cdr2_len - r###"BCR=85333 CDR3=CARDLRVEGFDYW CVARS=cdr1_len,cdr2_len AMINO="###, - // 122. test insertion in CDR1 and test cdr3_start when there is an insertion - r###"BCR=123089 CDR3=CARARPYSSGWSLDAFDIW AMINO=cdr1,cdr3 CVARSP=cdr1_aa - POUT=stdout PCOLS=cdr3_start1"###, - // 123. test fwr1_dna and fwr2_dna - r###"BCR=85333 CDR3=CARDLRVEGFDYW CVARSP=fwr1_dna,fwr2_dna AMINO=cdr3"###, - // 124. test fwr3_dna - r###"BCR=85333 CDR3=CARDLRVEGFDYW CVARSP=fwr3_dna AMINO=cdr3"###, - // 125. test fwr1_aa and fwr2_aa and fwr3_aa - r###"BCR=85333 CDR3=CARDLRVEGFDYW CVARSP=fwr1_aa,fwr2_aa,fwr3_aa AMINO=cdr3"###, - // 126. test fwr1_len and fwr2_len and fwr3_len - r###"BCR=85333 CDR3=CARDLRVEGFDYW CVARSP=fwr1_len,fwr2_len,fwr3_len AMINO=cdr3"###, - // 127. test 1/8 for fwr* in AMINO - r###"BCR=85333 CDR3=CARDLRVEGFDYW AMINO=var,share,donor,fwr1,cdr1"###, - // 128. test 2/8 for fwr* in AMINO - r###"BCR=85333 CDR3=CARDLRVEGFDYW AMINO=var,share,donor,cdr1,fwr2"###, - // 129. test 3/8 for fwr* in AMINO - r###"BCR=85333 CDR3=CARDLRVEGFDYW AMINO=var,share,donor,fwr2,cdr2"###, - // 130. test 4/8 for fwr* in AMINO - r###"BCR=85333 CDR3=CARDLRVEGFDYW AMINO=var,share,donor,cdr2,fwr3"###, - // 131. test 5/8 for fwr* in AMINO - r###"BCR=85333 CDR3=CARDLRVEGFDYW AMINO=var,share,donor,fwr3,cdr3"###, - // 132. test 6/8 for fwr* in AMINO - r###"BCR=85333 CDR3=CARDLRVEGFDYW AMINO=var,share,donor,fwr1,fwr2"###, - // 133. test 7/8 for fwr* in AMINO - r###"BCR=85333 CDR3=CARDLRVEGFDYW AMINO=var,share,donor,fwr2,fwr3"###, - // 134. test 8/8 for fwr* in AMINO - r###"BCR=85333 CDR3=CARDLRVEGFDYW AMINO=var,share,donor,fwr2,cdr2,fwr3"###, - // 135. test CONST_IGH - r###"BCR=123085 CDR3=CARPKSDYIIDAFDIW SEG=IGLV1-47 CONST_IGH="IGHG.""###, - // 136. test CONST_IGKL - r###"BCR=123085 CDR3=CARPKSDYIIDAFDIW SEG=IGLV1-47 CONST_IGKL=IGLC3"###, - // 137. test 1/2 of fwr4 - r###"BCR=85333 CDR3=CARDLRVEGFDYW AMINO=var,share,donor,cdr3,fwr4 CVARS=fwr4_aa"###, - // 138. test 2/2 of fwr4 - r###"BCR=85333 CDR3=CARDLRVEGFDYW CVARS=fwr4_dna,fwr4_len"###, - // 139. test cvar vj_seq_nl - r###"BCR=85333 CHAINS=1 CDR3=CAAWDDSLNGWVF POUT=stdout PCOLS=vj_seq_nl1"###, - // 140. test cvar vj_aa_nl - r###"BCR=85333 CHAINS=1 CDR3=CAAWDDSLNGWVF POUT=stdout PCOLS=vj_aa_nl1"###, - // 141. test cvar aa% - r###"BCR=85333 CDR3=CAKGDRTGYSYGGGIFDYW CVARS=aa%,dna%"###, - // 142. test 1/3 of DIFF_STYLE - r###"BCR=123085 CDR3=CARVRDILTGDYGMDVW DIFF_STYLE=C1"###, - // 143. test 2/3 of DIFF_STYLE - r###"BCR=123085 CDR3=CARVRDILTGDYGMDVW DIFF_STYLE=C2"###, - // 144. test 3/3 of DIFF_STYLE - r###"BCR=123085 CDR3=CAREPLYYDFWSAYFDYW DIFF_STYLE=C1"###, - // 145. test the lead variable "filter" - r###"BCR=123085 NALL LVARSP=filter PER_CELL CHAINS=2 CDR3=CQQSYSTPPYTF SEG=IGKV1D-39 - SEG=IGLV3-21"###, - // 146. test BUILT_IN - r###"BCR=../2.0/124550 CDR3=CAREPLYYDFWSAYFDYW BUILT_IN"###, - // 147. test NALL_GEX - r###"BCR=86237 GEX=85679 NALL_GEX LVARSP=n_gex,filter PER_CELL BARCODE=CTTGGCTGTTAAGACA-1"###, - // 148. test that LVARSP=n_gex fails if only BCR provided - r###"BCR=1031851 LVARSP=n_gex EXPECT_FAIL"###, - // 149. test FCELL with complex expression - r###"BCR=123085 BC=testx/inputs/123077_cells.csv PER_CELL LVARSP=keeper,rank - FCELL="keeper == 'no' && rank > 10""###, - // 150. test FCELL with a more complex expression - r###"BCR=123085 BC=testx/inputs/123077_cells.csv PER_CELL LVARSP=keeper,rank - FCELL="(keeper == 'no' && rank > 10) || keeper == 'maybe'""###, - // 151. test PEER_GROUP - r###"BCR=85333 CDR3=CAKGRYSSPQYYFDYW PEER_GROUP=stdout"###, - // 152. test PEER_GROUP with PG_READABLE - r###"BCR=85333 CDR3=CAKGRYSSPQYYFDYW PEER_GROUP=stdout PG_READABLE"###, - // 153. test d_start and d_frame - r###"BCR=86237 CDR3=CARGHPNYDYVWGSYRYRAYYFDYW POUT=stdouth - PCOLS=d_start1,d_frame1,d_start2,d_frame2"###, - // 154. test POUT=stdout with NOPRINT - r###"BCR=85333 CDR3="CARTSNRGIVATIFRAFDIW|CARDPRGWGVELLYYMDVW" NOPRINT POUT=stdout - PCOLS=cdr3_aa1"###, - // 155. test count_ and F for that - // Note that F is deprecated, equals KEEP_CLONO_IF_CELL_MEAN. - r###"BCR=123085 LVARSP="z:count_CAKTG" F="z > 0""###, - // 156. test ref variables - r###"BCR=123085 CDR3=CAREVEQWLERNTLDYW POUT=stdouth PCOLS=fwr1_aa1,fwr1_aa_ref1 AMINO=fwr1"###, - // 157. test ref variables - r##"BCR=123085 CDR3=CAREVEQWLERNTLDYW POUT=stdouth PCOLS=fwr1_dna1,fwr1_dna_ref1 AMINO=fwr1"##, - // 158. test ref variables - r###"BCR=123085 CDR3=CAREVEQWLERNTLDYW POUT=stdouth PCOLS=fwr2_aa1,fwr2_aa_ref1 AMINO=fwr2"###, - // 159. test ref variables - r##"BCR=123085 CDR3=CAREVEQWLERNTLDYW POUT=stdouth PCOLS=fwr2_dna1,fwr2_dna_ref1 AMINO=fwr2"##, - // 160. test ref variables - r###"BCR=123085 CDR3=CAREVEQWLERNTLDYW POUT=stdouth PCOLS=fwr3_aa1,fwr3_aa_ref1 AMINO=fwr3"###, - // 161. test ref variables - r##"BCR=123085 CDR3=CAREVEQWLERNTLDYW POUT=stdouth PCOLS=fwr3_dna1,fwr3_dna_ref1 AMINO=fwr3"##, - // 162. test ref variables - r###"BCR=123085 CDR3=CAREVEQWLERNTLDYW POUT=stdouth PCOLS=fwr4_aa1,fwr4_aa_ref1 AMINO=fwr4"###, - // 163. test ref variables - r###"BCR=123085 CDR3=CAREVEQWLERNTLDYW POUT=stdouth PCOLS=cdr1_aa2,cdr1_aa_ref2 AMINO=cdr1"###, - // 164. test ref variables - r##"BCR=123085 CDR3=CAREVEQWLERNTLDYW POUT=stdouth PCOLS=cdr1_dna2,cdr1_dna_ref2 AMINO=cdr1"##, - // 165. test ref variables - r###"BCR=123085 CDR3=CAREVEQWLERNTLDYW POUT=stdouth PCOLS=cdr2_aa2,cdr2_aa_ref2 AMINO=cdr2"###, - // 166. test ref variables - r##"BCR=123085 CDR3=CAREVEQWLERNTLDYW POUT=stdouth PCOLS=cdr2_dna2,cdr2_dna_ref2 AMINO=cdr2"##, - // 167. Test that for TCR, the number of two-chain clonotypes does not change. It is probably - // OK for it to change a little bit, but a big change would be indicative of a problem. At - // one point we had a release with such a problem and this test is here to prevent that from - // happening again. - r###"TCR=101287 NOPRINT REPROD REQUIRED_TWO_CHAIN_CLONOTYPES=849 EXPECT_OK"###, - // 168. Test POUT without PCELL, where a per-barcode variable is converted into a - // comma-separated list. - r###"BCR=123085 BC=testx/inputs/123077_cells.csv POUT=stdout PCOLS=rank - CDR3=CAKAGPTESGYYVWYFDLW MIN_CELLS=2"###, - // 169. this crashed at one point because the heavy chain CDR3 computed by cellranger was - // different than the current one, resulting in an inconsistency - r###"BCR=85333 CDR3=CQQYNSYSYTF CVARSP=fwr3_aa_ref"###, - // 170. doublet filter, before - r###"BCR=123085 CDR3=CAREGGVGVVTATDWYFDLW NDOUBLET"###, - // 171. doublet filter, after - r###"BCR=123085 CDR3=CAREGGVGVVTATDWYFDLW"###, - // 172. this crashed at one point - r###"META=testx/inputs/test11_meta LVARSP=CD56_ab NOPRINT EXPECT_OK"###, - // 173. test MIN_UMIS - r###"BCR=85333 MIN_UMIS=100"###, - // 174. test METAX, and also the origins printed by this was wrong at one point - r###"METAX="bcr,origin,donor;toast:86237,c,d;zip:123085,a,b" LVARSP=origins,donors - POUT=stdouth PCOLS=origins,donors CDR3=CARSFFGDTAMVMFQAFDPW"###, - // 175. test some variables - r###"BCR=123085 CDR3=CAKDKVPRRSSWSVFDYYGMDVW POUT=stdouth PCOLS=cdr1_aa1,cdr1_aa_1_2_ext1"###, - // 176. test some variables - r###"BCR=123085 CDR3=CAKDKVPRRSSWSVFDYYGMDVW POUT=stdouth PCOLS=cdr2_aa1,cdr2_aa_1_2_ext1"###, - // 177. test some variables - r###"BCR=123085 CDR3=CAKDKVPRRSSWSVFDYYGMDVW POUT=stdouth PCOLS=cdr3_aa1,cdr3_aa_1_2_ext1"###, - // 178. test an ndiff variable as a parseable variable - r###"BCR=123085 CDR3=CAKDKVPRRSSWSVFDYYGMDVW POUT=stdouth PCOLS=ndiff1vj1"###, - // 179. test cdr1_aa_north etc. - r###"BCR=123085 CDR3=CAKDKVPRRSSWSVFDYYGMDVW POUT=stdouth - PCOLS=cdr1_aa_north1,cdr1_aa_north2,cdr2_aa_north1,cdr2_aa_north2,cdr3_aa_north1,cdr3_aa_north2"###, - // 180. test some count vars - r###"BCR=85333 LVARS=all:count_C,c:count_cdr_C,c1:count_cdr1_C,c3:count_cdr3_C,f:count_fwr_C,f1:count_fwr1_C CDR3=CARDKEGLSGYAVERAFDYW"###, - // 181. test some count vars - r###"BCR=85333 LVARS=f2:count_fwr2_C CDR3=CVKDIRESSGPLLSHSFDLW"###, - // 182. test some count vars - r###"BCR=85333 LVARS=f3:count_fwr3_C CDR3=CARGGFSHAFDIW"###, - // 183. test some count vars - r###"BCR=123085 LVARS=f4:count_fwr4_V CDR3=CTRDRDLRGATDAFDIW"###, - // 184. test some count vars - r###"BCR=123085 LVARS=c2:count_cdr2_C CDR3=CARQQDVYTRSWYFDYW CELLS=1"###, - // 185. test SUPPRESS_ISOTYPE_LEGEND - r###"BCR=123085 MIN_CELLS=10 PLOT_BY_ISOTYPE=stdout NOPRINT MIN_CHAINS_EXACT=2 - SUPPRESS_ISOTYPE_LEGEND"###, - // 186. test LVAR= (with no value) - r###"BCR=123085 CDR3=CAREPLYYDFWSAYFDYW LVARS="###, - // 187. test FOLD_HEADERS - r###"BCR=123085 CDR3=CAREADYCSGGSCYFSDW FOLD_HEADERS AMINO=cdr3 CVARS=u"###, - // 188. test for correct handling of COMPLETE + r_cell1 (asserted at one point) - r###"BCR=85333 POUT=stdout PCOLS=r_cell1 COMPLETE PCELL CDR3=CARGQEGSGWYRPWDYW"###, - // 189. test CONP - r###"BCR=123085 CONP CDR3=CVKRASGSAFTAPYW"###, - // 190. test CONX - r###"BCR=123085 CONX CDR3=CVKRASGSAFTAPYW"###, - // 191. test CONP when there's a gap - r###"BCR=123085 CONP CDR3=CALGGYTWFDPW"###, - // 192. test INFO - r###"BCR=123085 CDR3=CAREGGVGVVTATDWYFDLW INFO=testx/inputs/123085_info.csv LVARSP=funny"###, - // 193. check that this fails gracefully - r###"NOPRINT EXPECT_FAIL"###, - // 194. this crashed at one point - r###"BCR=86237 GEX=85679 LVARSP=g37:IGHV3-7_g_μ NH5 POUT=stdout PCOLS=g37 EXPECT_OK"###, - // 195. failed at one point - r###"BCR=86237 GEX=85679 LVARSP=woof:IGHV3-7_g_μ NH5 POUT=stdout PCOLS=woof EXPECT_OK"###, - // 196. test TREE=n - r###"BCR=123085 COMPLETE TREE=n CDR3=CARDLGGRYYGSKDPW"###, - // 197. failed at one point - r###"BCR=123085 INFO=testx/inputs/123085_info.csv LVARSP=funny EXPECT_OK"###, - // 198. test TREE=n,cdr2_aa1 - r###"BCR=123085 AMINO=cdr3 CDR3=CAVTIFGVRTALPYYYALDVW TREE=n,cdr2_aa1"###, - // 199. test KEEP_CLONO_IF_CELL_MEAN with INFO - r###"BCR=123085 INFO=testx/inputs/123085_info.csv LVARSP=moo - KEEP_CLONO_IF_CELL_MEAN="moo>0""###, - // 200. test SCAN_EXACT - r###"BCR=123085 GEX=123217 LVARSP=IGHV1-69D_g_μ,IGHV3-64D_g_μ MIN_CELLS=10 - SCAN="(IGHV1-69D_g_μ)>=1800,(IGHV3-64D_g_μ)>=100,t-10*c>=5.0" NOPRINT H5 SCAN_EXACT"###, - // 201. test SOURCE - r###"SOURCE=testx/inputs/123085_args AMINO=cdr2,cdr3"###, - // 202. DUPLICATE TO REPLACE - r###"SOURCE=testx/inputs/123085_args AMINO=cdr2,cdr3 EXPECT_OK"###, - // 203. test plotting with using the BC option to set color - r###"BCR=123085 BC=testx/inputs/123077_cells.csv PLOT=stdout NOPRINT"###, - // - // TESTS WITH PER_CELL AND PCELL - // - // 204. test INFO with PER_CELL and PCELL - r###"BCR=123085 CDR3=CAREGGVGVVTATDWYFDLW INFO=testx/inputs/123085_info.csv POUT=stdout - PCOLS=moo LVARS=moo PCELL PER_CELL"###, - // 205. test g with PER_CELL and PCELL - r###"BCR=123085 GEX=123217 AMINO=cdr3 LVARS=g15 CDR3=CARVRDILTGDYGMDVW POUT=stdout PCOLS=g15 - PCELL PER_CELL H5"###, - // 206. test origins with PER_CELL and PCELL - r###"BCR=123085:123089 AMINO= CDR3=CTRAGFLSYQLLSYYYYGMDVW FOLD_HEADERS POUT=stdout PCELL - PER_CELL PCOLS=origins LVARSP=origins"###, - // 207. test datasets with PER_CELL and PCELL - r###"BCR=123085:123089 CELLS=5 AMINO= CDR3=CTRAGFLSYQLLSYYYYGMDVW FOLD_HEADERS POUT=stdout - PCELL PER_CELL PCOLS=datasets LVARSP=datasets"###, - // 208. test donors with PER_CELL and PCELL - r###"BCR="123085;123089" AMINO= CDR3=CTRAGFLSYQLLSYYYYGMDVW FOLD_HEADERS POUT=stdout PCELL - PER_CELL PCOLS=donors LVARS=donors MIX_DONORS CHAINS=2"###, - // 209. test n with PER_CELL and PCELL - r###"BCR=123085 AMINO=cdr3 CDR3=CAKDKVPRRSSWSVFDYYGMDVW POUT=stdout PCELL PER_CELL PCOLS=n"###, - // 210. test filter with PER_CELL and PCELL - r###"BCR=123085 AMINO=cdr3 FOLD_HEADERS POUT=stdout PCELL PER_CELL PCOLS=filter LVARSP=filter - NALL_CELL CDR3=CAKHQRGGGRQNYYYGMDVW"###, - // 211. test inkt with PER_CELL and PCELL - r###"TCR=101287 INKT MIN_CELLS=2 AMINO=cdr3 FOLD_HEADERS POUT=stdout PCELL PER_CELL - PCOLS=inkt LVARSP=inkt"###, - // 212. test mait with PER_CELL and PCELL - r###"TCR=101287 AMINO=cdr3 FOLD_HEADERS POUT=stdout PCELL PER_CELL PCOLS=mait LVARSP=mait - CDR3=CSAGQGDTEAFF"###, - // 213. test cred with PER_CELL and PCELL - r###"BCR=123085 GEX=123217 AMINO=cdr3 LVARS=cred CVARS=u POUT=stdout PCOLS=cred,cred_cell - PCELL PER_CELL H5 CDR3=CARDPEDIVLMVYAMGGNYGMDVW"###, - // 214. test n_ with PER_CELL and PCELL - r###"BCR=123085:123089 AMINO=cdr3 FOLD_HEADERS POUT=stdout PCELL PER_CELL PCOLS=n_s1 - LVARS=datasets,n_s1 CDR3=CARDLFVLVPAAITYYYGMDVW CVARS=u"###, - // 215. test n_gex with PER_CELL and PCELL - r###"BCR=123085 GEX=123217 AMINO=cdr3 LVARS=n_gex POUT=stdout PCOLS=n_gex,n_gex_cell PCELL - PER_CELL H5 CDR3=CAKDKVPRRSSWSVFDYYGMDVW"###, - // 216. test near with PER_CELL and PCELL - r###"BCR=123085 AMINO=cdr3 POUT=stdout PCELL PER_CELL LVARSP=near PCOLS=near CVARS=u - CDR3=CARHLQWELPYW"###, - // 217. test far with PER_CELL and PCELL - r###"BCR=123085 AMINO=cdr3 POUT=stdout PCELL PER_CELL LVARSP=far PCOLS=far CVARS=u - CDR3=CARHLQWELPYW"###, - // 218. test dref with PER_CELL and PCELL - r###"BCR=123085 AMINO=cdr3 POUT=stdout PCELL PER_CELL LVARSP=dref PCOLS=dref CVARS=u - CDR3=CSRVFGNSTYYSSRVGGYW"###, - // 219. test count_cdr_C with PER_CELL and PCELL - r###"BCR=85333 LVARSP=count_cdr_C CDR3=CARDKEGLSGYAVERAFDYW POUT=stdout PCELL PER_CELL - PCOLS=count_cdr_C CVARS=u"###, - // 220. test cdr3_aa_conp with PER_CELL and PCELL - r###"BCR=123085 AMINO= CDR3=CARHLQWELPYW FOLD_HEADERS POUT=stdout PCELL PER_CELL - PCOLS=cdr3_aa_conp2 CVARS=cdr3_aa_conp"###, - // 221. test RPS27_g with PER_CELL and PCELL - r###"BCR=123085 GEX=123217 AMINO=cdr3 POUT=stdout PCOLS=RPS27_g,RPS27_g_cell PCELL - PER_CELL H5 CDR3=CAREVEQWLERNTLDYW LVARSP=RPS27_g"###, - // - // OTHER TESTS - // - // 222. test for busted reference - r###"BCR=85333 REF=testx/inputs/busted_regions.fa EXPECT_FAIL"###, - // 223. test {v,d,j}_name and _id - r###"BCR=86237 CDR3=CARGHPNYDYVWGSYRYRAYYFDYW POUT=stdouth - PCOLS=v_name1,d_name1,j_name1,v_id1,d_id1,j_id1"###, - // 224. test const_id and utr_name - r###"BCR=86237 CDR3=CARSFFGDTAMVMFQAFDPW POUT=stdouth - PCOLS=const_id1,utr_name1"###, - // 225. test q_ - r###"BCR=123085 CDR3=CANFGRGGDVAFDIW CVARS=q10_"###, - // - // MORE TESTS OF PER_CELL AND PCELL - // - // 226. test RPS27_g_mean with PER_CELL and PCELL - r###"BCR=123085 GEX=123217 AMINO=cdr3 POUT=stdout PCOLS=RPS27_g_mean PCELL PER_CELL H5 - CDR3=CAREVEQWLERNTLDYW LVARSP=RPS27_g_mean CVARS=u"###, - // 227. test datasets, donors, origins with PER_CELL and PCELL - r###"BCR=123085:123089 CELLS=5 AMINO= CDR3=CTRAGFLSYQLLSYYYYGMDVW FOLD_HEADERS POUT=stdout - PCELL PER_CELL PCOLS=datasets,datasets_cell,origins,origins_cell,donors,donors_cell - LVARSP=origins,donors"###, - // 228. test clonotype_ncells with PER_CELL and PCELL - r###"BCR=123085 AMINO= CDR3=CARHLQWELPYW FOLD_HEADERS POUT=stdout PCELL PER_CELL - PCOLS=clonotype_ncells LVARSP=clonotype_ncells"###, - // - // OTHER TESTS - // - // 229. test KEEP_CLONO_IF_CELL_MAX with comp - r###"BCR=123085 CVARSP=comp KEEP_CLONO_IF_CELL_MAX="comp1 >= 18" AMINO=cdr3"###, - // 230. not really clear what this is doing, but don't delete, as it used to represent - // strange behavior - r###"BCR=123085 CDR3=CTRDRDLRGATDAFDIW"###, - // 231. test ≤ - r###"BCR=86237 KEEP_CLONO_IF_CELL_MEAN="u2≤150" NOPRINT SUMMARY SUMMARY_CLEAN"###, - // 232. test nonsense variable in linear constraint - r###"BCR=86237 KEEP_CLONO_IF_CELL_MAX="gexzz > 8000" EXPECT_FAIL H5"###, - // 233. test use of two linear constraints - r###"BCR=123085 GEX=123217 - KEEP_CLONO_IF_CELL_MAX="gex > 8000" KEEP_CLONO_IF_CELL_MAX="gex < 8200" H5"###, - // 234. test tooltip comments; this is via a testing-only filename option gui_stdout - r###"BCR=123085 MIN_CELLS=10 PLOT_BY_ISOTYPE=gui_stdout NOPRINT MIN_CHAINS_EXACT=2"###, - // 235. test that v_name etc. do not appear in parseable output if chain is absent - r###"BCR=123085 CDR3=CVRGLRTW PCOLS=barcodes,v_name1,j_name1,v_id1,j_id1 POUT=stdouth"###, - // 236. test MAX_HEAVIES=1 - r###"BCR=123085 CDR3=CASPVPYYYDSSGYPYW MAX_HEAVIES=1 EXPECT_NULL"###, - // 237. test enclone --help - r###"--help NO_PRE EXPECT_OK"###, - // 238. test cigar - r###"BCR=123085 AMINO=cdr3 POUT=stdout PCOLS=cigar2 CDR3=CTRSSTTPRDPTMIVVAYYYYGMDVW"###, - // 239. test group post filtering - r###"BCR=123085 G=2,100-101 NGROUP"###, - // 240. test sym option for PLOTXY_EXACT - r###"BCR=123085 PLOTXY_EXACT=u1,u2,stdout,sym NOPRINT"###, - // 241. test KEEP_CELL_IF on gex var - r###"BCR=123085 GEX=123217 LVARSP=IGHM_g KEEP_CELL_IF="IGHM_g>=10" CDR3=CARRYFGVVADAFDIW H5"###, - // 242. test nchains_present - r###"BCR=86237 LVARSP=nchains_present CDR3=CARSFFGDTAMVMFQAFDPW"###, - // 243. this crashed at one point - r###"BCR=123085 GROUP="cdr3_aa_heavy>=85%,vj_refname" MIN_GROUP=2 PLOT=/dev/null - NOPRINT EXPECT_OK"###, - // 244. test for very long (120 amino acid) CDR3 - // Note that this long CDR3 is likely part of a nonproductive chain. The test is here because - // there may be long productive CDR3 sequences in data from other species, although we do not - // have such data. This is from 1020665. - r###"BCR=testx/inputs/flaky BUILT_IN REPROD CVARSP=cdr3_len CDR3=CARDGGGQPFDLW AMINO="###, - // 245. Test a tweak to the weak chains filter. This should have two chains. From 174957. - r###"BCR=testx/inputs/flaky2 CDR3=CARPRGYCSGGSCFPFASW BUILT_IN"###, - // 246. test that used to crash on a particular barcode; this also gave the wrong - // answer for an insertion until it was fixed - r###"BCR=testx/inputs/flaky3 NCELL CDR3=CARNWRYCTSVSCQHREYFYYMDVW AMINO=cdr3"###, - // 247. this crashed - r###"BCR=testx/inputs/flaky4"###, - // 248. this crashed - r###"BCR=testx/inputs/flaky5"###, - // 249. an example that triggered an internal inconsistency test, which we subsequently removed; - // there are three chains and the middle one was the problem - r###"TCR=testx/inputs/flaky6 BARCODE=CCAGCGAAGTGTTGAA-1 REPROD EXPECT_OK"###, - // 250. test MOUSE + IMGT; note that specifying by number forces BCR+TCR reference checks - // Added FORCE_EXTERNAL because couldn't reproduce the result. Don't understand. - r###"74396 MOUSE NOPRINT SUMMARY SUMMARY_CLEAN IMGT ACCEPT_BROKEN FORCE_EXTERNAL"###, - // 251. test mouse + IMGT; note that specifying by number forces BCR+TCR reference checks - r###"74396 MOUSE REQUIRE_UNBROKEN_OK IMGT ACCEPT_BROKEN EXPECT_NULL"###, - // 252. this exhibits what happens when signature filtering is ON, see next - // this was the only example we could find - // based on 83808-83809, derived using modified version of minimal_fail, and also shrink_json - r###"BCR=testx/inputs/flaky7 BUILT_IN REPROD REQUIRED_TWO_CHAIN_CLONOTYPES=1 - REQUIRED_THREE_CHAIN_CLONOTYPES=0 NOPRINT EXPECT_OK"###, - // 253. this exhibits what happens when signature filtering is OFF, see previous - // this was the only example we could find - // based on 83808-83809, derived using modified version of minimal_fail, and also shrink_json - r###"BCR=testx/inputs/flaky7 BUILT_IN REPROD NSIG REQUIRED_TWO_CHAIN_CLONOTYPES=0 - REQUIRED_THREE_CHAIN_CLONOTYPES=1 NOPRINT EXPECT_OK"###, - // 254. parseable value for fwr4_aa was wrong, from 1117070 - r###"BCR=testx/inputs/flaky AMINO=fwr4 CDR3=CAKDVNGYSSGWAFENW POUT=stdout PCOLS=fwr4_aa1 - BUILT_IN"###, - // 255. conp value was truncated, from 1117069 - r###"BCR=testx/inputs/flaky CONP CDR3=CVRDPPEELELFDYW BUILT_IN"###, - // 256. Make sure that FP join output includes join error details. - // If somehow we fix the FP join occurring here, another one should be substituted. - // This is from BCR="131036;140707". - r###"PRE=testx/inputs BCR="flaky8a;flaky8b" ANN SHOW_BC MIN_DONORS=2 - PRINT_FAILED_JOINS BUILT_IN NO_PRE"###, - // 257. clonotype that was two clonotypes before raising MAX_DIFFS to 60, from 1084461-1084462 - r###"BCR=testx/inputs/flaky CDR3=CAKEFGNGGFDTFDIW BUILT_IN AMINO=cdr3"###, - // 258. This used to appear as a four-chain clonotype, and is now split. From 123085,123090. - r###"BCR=testx/inputs/flaky9 BUILT_IN REQUIRED_FOUR_CHAIN_CLONOTYPES=0 EXPECT_OK"###, - // 259. this crashed at one point, from 83809 - r###"BCR=testx/inputs/flaky10 EXPECT_OK"###, - // 260. the result of this changed when sub_alts was changed, from 40086;132888 - r###"BCR=testx/inputs/flaky11 MAX_DIFFS=80 CDR3=CVKGDWGSAFDIW BUILT_IN"###, - // 261. previously this yielded a disconnected clonotype, from 140699,140705-140706 - r###"BCR=testx/inputs/flaky12 AMINO=cdr3 CDR3="CAKDRQAGGIGEVDDW|CARDRVPGGIGEVDYW" BUILT_IN"###, - // 262. test NSEG - r###"BCR=86237 SEG=IGHV4-59 NSEG="IGHJ3|IGHJ4|IGHJ6""###, - // 263. test NSEGN - r###"BCR=86237 SEG=IGHV4-34 NSEGN="51|54|55|57|321""###, - // 264. test MIN_ORIGINS - r###"BCR=123085:123089 MAX_CELLS=2 SEG=IGHV3-49 MIN_ORIGINS=2"###, - // 265. test DVARS - // The output is a bit flaky because we imported some but not all of the special files - // for 85679. - r###"BCR=86237 GEX=85679 DVARS=CD19_ab_cellular_u,CD19_ab_cellular_r - NOPRINT SUMMARY SUMMARY_CLEAN"###, - // 266. a test of VAR_DEF - r###"BCR=86237 GEX=85679 VAR_DEF="mu:CD19_ab + CD25_ab" LVARSP=gex,CD19_ab,CD25_ab,mu - CDR3=CARSFFGDTAMVMFQAFDPW FOLD_HEADERS PER_CELL AMINO="###, - // 267. a test of VAR_DEF - r###"BCR=86237 GEX=85679 VAR_DEF=x19:CD19_ab VAR_DEF=x25:CD25_ab VAR_DEF="mu:x19 + x25" - LVARSP=gex,CD19_ab,CD25_ab,mu CDR3=CARSFFGDTAMVMFQAFDPW FOLD_HEADERS PER_CELL AMINO="###, - // 268. a test of VAR_DEF - r###"BCR=86237 GEX=85679 VAR_DEF="pink:PINK1-AS_g" LVARSP=pink CDR3=CARSFFGDTAMVMFQAFDPW - FOLD_HEADERS PER_CELL AMINO="###, - // 269. test fb variables - r###"BCR=86237 GEX=85679 ALLOW_INCONSISTENT NGEX LVARSP=fb1,fb1_n PER_CELL AMINO=cdr3 CVARS= FOLD_HEADERS POUT=stdouth PCOLS=fb2,fb2_n,fb2_n_cell PCELL CDR3=CARSFFGDTAMVMFQAFDPW"###, - // 270. test NOSPACES - r###"BCR=123085 CDR3=CTRDRDLRGATDAFDIW AMINO=cdr3,fwr4 NOSPACES CONX"###, - // 271. test for weird path bug - r###"BCR_GEX=tiny_multi_PD_broken EXPECT_OK"###, - // 272. a test for validated UMI variables - r###"BCR=tiny_multi_PD CVARS=u,nval,nnval,nival BARCODE=AAAGCAAGTGGCTCCA-1 AMINO= PER_CELL - POUT=stdouth PCOLS=nval1,nval2,nval3,valumis3,valbcumis2"###, - // 273. a test for validated UMI variables - r###"BCR=tiny_multi_PD CVARS=u,nval,nnval,nival AMINO= PER_CELL POUT=stdouth - PCOLS=ivalumis1,ivalbcumis1,nvalbcumis2 BARCODE=TACCTTAAGAGCCCAA-1"###, - // 274. at one point this printed bell characters - r###"CVARS=u,nval,nnval,nival AMINO= PER_CELL POUT=stdouth PCOLS=nval1,nval2 BCR=123085 - BARCODE=ACAGCCGAGATAGGAG-1"###, - // 275. test _ext var with negative extensions - r###"BCR=123085 CDR3=CAKDKVPRRSSWSVFDYYGMDVW POUT=stdouth - PCOLS=cdr3_aa1,cdr3_aa_-1_-2_ext1"###, - // 276. this failed at one time - r###"BCR=40970_subset NCELL NOPRINT EXPECT_OK"###, - // 277. test nbc - r###"BCR=85333 CDR3=CARDGMTTVTTTAYYGMDVW LVARSP=nbc PER_CELL CVARS= FOLD_HEADERS"###, - // 278. test some count_fwr variables - r###"BCR=85333 LVARS=count_fwr1_C,count_fwr_C CDR3=CARGGFSHAFDIW AMINO=cdr3"###, - // 279. barcode having five contigs - r###"BCR=123085 NALL CDR3=CAKKHYRYYDSSGYNPLGYYYYGMDVW CVARS=u AMINO= FOLD_HEADERS"###, - // 280. this asserted at one point - r###"BCR=86237 CDR3=CARRGPRFRPRFLRGRKTGNWFDPW CVARS= AMINO= EXPECT_FAIL"###, - // 281. this yielded the wrong aa_nl_2 value - r###"BCR=123085 CDR3=CARHPAPNYGFWSGYYKTDNWFDPW POUT=stdout PCOLS=vj_aa_nl2 CVARS=u,notes - AMINO=fwr1"###, - // 282. fwr3_aa1 was wrong - r###"BCR=123085 CDR3=CALGGYTWFDPW POUT=stdout PCOLS=fwr3_aa1"###, - // 283. another test of VAR_DEF - r###"BCR=86237 GEX=85679 VAR_DEF="mu:CD19_ab + CD25_ab" LVARSP=gex,CD19_ab,CD25_ab,mu - CDR3=CARSFFGDTAMVMFQAFDPW FOLD_HEADERS PER_CELL AMINO= POUT=stdout PCOLS=mu"###, - // 284. another test of VAR_DEF - r###"BCR=86237 GEX=85679 VAR_DEF="mu:CD19_ab + CD25_ab" LVARSP=mu CDR3=CARSFFGDTAMVMFQAFDPW - PER_CELL POUT=stdout PCOLS=mu PCELL FOLD_HEADERS"###, - // 285. another test of VAR_DEF - r###"BCR=123085 VAR_DEF=x:u1 LVARSP=x CDR3=CAKDGYSSSWYVVDW SEG=IGHV3-30"###, - // 286. this asserted at one point - r###"BUILT_IN BCR=testx/inputs/flaky2/outs/,testx/inputs/flaky3/outs/ EXPECT_OK"###, - // 287. test gamma delta data (pos control) - r###"TCRGD=testx/inputs/gamma_delta1 GAMMA_DELTA MOUSE BUILT_IN"###, - // 288. test gamma delta data without GAMMA_DELTA tag in regular TCR pipe (neg control) - r###"TCR=testx/inputs/gamma_delta1 MOUSE BUILT_IN REQUIRED_CLONOTYPES=0 EXPECT_NULL"###, - // 289. test dref_max - r###"BCR=86237 LVARSP=dref_max CDR3=CARAPEDTSRWPQYNYSGLDVW AMINO=cdr3"###, - // 290. test v_name_orig - r###"BCR=123089 CVARS=v_name_orig PCELL POUT=stdout PCOLS=v_name_orig_cell2 PER_CELL - CDR3=CARDRIDDSSGYYYAYYYGMDVW"###, - // 291. test SPLIT_PLOT_BY_DATASET - r###"BCR=123085,123089 PLOT_BY_ISOTYPE=stdout SPLIT_PLOT_BY_DATASET NOPRINT"###, - // 292. this asserted - r###"BCR=85333 CDR3=”CAKGDRTGYSYGGGIFDYW~3” NOPRINT SUMMARY EXPECT_FAIL"###, - // 293. test BC var in color by variable - r###"BCR=123085 BC=testx/inputs/123077_cells.csv KEEP_CELL_IF="rank >= 1" - HONEY="out=stdout,color=var,rank" NOPRINT"###, - // 294. this asserted - r###"BCR=86237 HONEY=out=stdout,color=var,cdr3_aa1 NOPRINT EXPECT_FAIL"###, - // 295. test BC_JOINT - r###"BCR="123085;85333" BC_JOINT=testx/inputs/bc_joint.csv KEEP_CELL_IF="dummy >= 0""###, - // 296. test META with two args - r###"META=testx/inputs/meta1.csv,testx/inputs/meta2.csv CDR3="CQQANSFPLTF|CQHYGSSPYTF" - SEG=IGHV4-39"###, - // 297. test two META args - r###"META=testx/inputs/meta1.csv META=testx/inputs/meta2.csv CDR3="CQQANSFPLTF|CQHYGSSPYTF" - SEG=IGHV4-39"###, - // 298. test iReceptor and PREPOST - r###"PREPOST=iReceptor BUILT_IN BCR=CIS/1_1 CDR3=CARIPYGDYWLGPKHWYFDLW"###, - // 299. test PNOHEADER - r###"BCR=85333 CDR3=CARDGMTTVTTTAYYGMDVW POUT=stdout PCOLS=dref PNO_HEADER NOPRINT"###, - // 300. test PNOHEADER - r###"BCR=85333 CDR3=CARDGMTTVTTTAYYGMDVW POUT=stdouth PCOLS=dref PNO_HEADER NOPRINT"###, - // 301. test DATASET - r###"BCR="86237;123085,123089" CELLS=1 SEG=IGHV4-34 SEG=IGKV1D-39 NGROUP - DATASET="123085|123089""###, - // 302. test hcomp and jun_ins and jun_mat and jun_sub - r###"BCR=85333 JALIGN1 CHAINS_EXACT=2 CDR3=CAKGDRTGYSYGGGIFDYW - LVARSP=hcomp,jun_ins,jun_mat,jun_sub AMINO=cdr3 FOLD_HEADERS"###, - // 303. test GD_BC - r###"BCR=testx/inputs/flaky GD_BC=testx/inputs/flaky NO_PRE BUILT_IN AMINO=cdr3 - LVARSP=status PER_CELL CDR3=CVRDPPEELELFDYW"###, - // 304. test Ab-only data - r###"BCR=1031851 GEX=1031779 NGEX LVARSP=n_gex,CD19_ab - CDR3="CARDELDILTGYNIPTFGGCVYW|CAHHGSARYSSSWHAAPGPYYFDYW" BUILT_IN"###, - // 305. test that LVARSP=gex fails on Ab-only data - r###"BCR=1031851 GEX=1031779 NGEX LVARSP=gex EXPECT_FAIL"###, -]; diff --git a/enclone_ranger/src/main_enclone.rs b/enclone_ranger/src/main_enclone.rs index b2417e352..7503db178 100644 --- a/enclone_ranger/src/main_enclone.rs +++ b/enclone_ranger/src/main_enclone.rs @@ -101,7 +101,6 @@ pub fn main_enclone_setup_ranger(args: &[String]) -> Result