 Diljot Grewal | 1e59ac7e350 | bugfix: only attempt to plot segments if there is data to plot | | |
Diljot Grewal | e2abfba5f02 | documentation:updated test dataset | | |
Diljot Grewal | 0e006ebf9cd | version bump | | |
 Pascale Walters | 7bb489154e4 | removed classifier, added ploidy option | | |
Diljot Grewal | e577415b307 | bugfix:issues with config generation | | |
Diljot Grewal | 237d64f8783 | fix:added haploid poison to hmmcopy | | |
Diljot Grewal | 08fd26a0192 | feature: increased mem on retries | | |
Diljot Grewal | 4d2a8868d56 | config: updated to use block style in output for readability, exposed all params to override | | |
Diljot Grewal | b5fe304f190 | feature: added classifier to hmmcopy | | |
Diljot Grewal | 52ad39c0b85 | bugfix: plotting errors when no segments | | |
Diljot Grewal | acac4b2d8a2 | added documentation | | |
Pascale Walters | 973f5143a92 | bug fix: remove broken segments dataframe handling | | |
Diljot Grewal | 96b369bf423 | fix: error handling for empty segments table | | |
Diljot Grewal | 6276c5423fe | bugfix: pandas sum adds nan to 0 | | |
Diljot Grewal | 7d6b51a243e | bugfix: reading by chunks can split sample across chunks that need to be merged together later | | |
 Andrew McPherson | 98e618c40e8 | minor: on disk merging of variant counts | | |
Andrew McPherson | f16f9a519cb | minor: pseudo wgs fixes | | |
 Ubuntu | 30e438872d3 | minor: small bug fix in strelka | | |
Andrew McPherson | fecd1bdb399 | feature: variant counting workflow | | |
Diljot Grewal | 3e8eb36cf25 | minor:set default aligner to bwa mem | | |
Diljot Grewal | d551457f1aa | bugfix: generate colormap for cellcalls in filtered data, not all calls before filters | | |
Diljot Grewal | aa98e0816a1 | minor: updated metrics heatmap colormap | | |
Diljot Grewal | dd457f0960c | minor: reduced segs plot size, single color legend per page | | |
Diljot Grewal | 17718eac65a | minor: moved segs and bias plots into separate dirs | | |
Diljot Grewal | d2bf99b5134 | hmmcopy_plots: same colormap for heatmap and hmmcopy, same colormap for all 6 multipliers in segs plot | | |
Diljot Grewal | 915c440355e | metrics_plot: center heatmap around 250k for total reads | | |
Diljot Grewal | 3922241983a | bugfix: at indexing doesnt work with categorical indexes in pandas, making cell id categorical breaks some code | | |
 Diljot Grewal | 2a0a576f71c | minor: updated dtypes for segments h5 merge | | |
Diljot Grewal | ea0d4d1da2f | bugfix: missing cellid column in failed hmmcopy segs | | |
Diljot Grewal | dc3b25e6dc6 | bugfix: making cellid categorical to improve compression and avoid itemsize errors, small fix in func path in alignment | | |
Diljot Grewal | afe57cfbeb1 | minor: fixed an issue with batch | | |
Diljot Grewal | 0efd3354f2f | bugfix: env vars should be upper case | | |
Diljot Grewal | 2ea28ce4079 | minor: fixed config generators | | |
Diljot Grewal | b86104cce13 | version bump | | |
Diljot Grewal | d4318dfd134 | minor: added white bars to heatmap for low mappability regions | | |
Diljot Grewal | c015fee1ce2 | minor: small fix in hmmcopy merge. | | |
Diljot Grewal | 47e5b31d06d | bugfix: density plots were missing one state, increased scatter point size in segs plot | | |
Diljot Grewal | 937c1c7c0af | minor: check for cases where a whole row is filtered out when merging hmmcopy pdfs | | |
Diljot Grewal | 42005ef972a | feature: one file per row for hmmcopy plots, sorted by column | | |
Diljot Grewal | 95b4c5ab022 | feature: reimplemented config and batch generation codee | | |
Diljot Grewal | dc1a0bb5cf0 | improvement: replaced all hardcoded human chromosomes with chroms from config | | |
Diljot Grewal | 1b445983992 | minor: converted some other functions to string, removed matplotlib from utils import, pysam moved to separate module from helpers | | |
Diljot Grewal | 64b617f2c95 | minor: renamed pseudo_wgs to merge bams workflow | | |
Diljot Grewal | 5e52b5005b8 | minor: removed unused remixt workflow | | |
Diljot Grewal | c3855b53aa4 | improvement: switch to strings for function in transform to avoid imports on head node | | |
Diljot Grewal | 3573f825c24 | feature: added an option to split bam files by reads | | |
Diljot Grewal | b870d5788d1 | bugfix: replaced hardcoded hmmcopy ref files in config | | |
Diljot Grewal | 90d2e5a66f1 | fix: parsing was broken for clean_sentinels and generate_config | | |
Diljot Grewal | bc7a6fc868e | minor: renamed pick_met and condition back to their original names | | |
Ubuntu | 1ed13b2b87d | bugfix: another fix in hmmcopy script | | |
