search

FelixKrueger / SNPsplit

Allele-specific alignment sorting
http://felixkrueger.github.io/SNPsplit/
GNU General Public License v3.0
52 stars 20 forks source link

Stats in YAML format to enable integration into MultiQC #29

Closed FelixKrueger closed 4 years ago

FelixKrueger commented 4 years ago

Phil asked if we could produce the stats in YAML format to make it easier to integrate into MultiQC https://github.com/ewels/MultiQC/pull/593#issuecomment-555764517

FelixKrueger commented 4 years ago

I have now updated the YAML report to include some Metadata (as requested here: https://github.com/ewels/MultiQC/pull/593#issuecomment-557804044). A sample YAML report now looks like this:

---
Meta:
  tool: SNPsplit
  version: 0.3.4_dev
  infile: lane4904.hicup.bam
  date_run: Mon Nov 25 15:37:32 2019
  mode: Hi-C
  library: paired-end
  command: SNPsplit --snp all_SNPs_CAST_EiJ_GRCm38.txt.gz lane4904.hicup.bam --hic
Tagging:
  total_reads: 1616940
  unaligned: 0
  percent_unaligned: 0.00
  g1: 391351
  percent_g1: 24.20
  g2: 358019
  percent_g2: 22.14
  unassignable: 864197
  percent_unassignable: 53.45
  no_snp: 2407
  percent_no_snp: 0.15
  bizarre: 3373
  percent_bizarre: 0.21
  SNP_annotation: all_SNPs_CAST_EiJ_GRCm38.txt.gz
  SNPs_stored: 20668547
  N_containing_reads: 754253
  non_N_containing_reads: 861790
  N_deletion: 897
  percent_N_deletion: 0.06
  multi_N_deletion: 1
  N_was_known_SNP: 1430442
  percent_N_was_known_SNP: 99.97
  N_not_known: 466
  percent_N_not_known: 0.03
Sorting:
  tagged_infile: lane4904.hicup.allele_flagged.bam
  HiC_total_pairs: 808470
  HiC_unassignable_UA_UA: 236613
  HiC_percent_unassignable_UA_UA: 29.27
  HiC_genome1_G1_G1: 89316
  HiC_percent_genome1_G1_G1: 11.05
  HiC_genome2_G2_G2: 81093
  HiC_percent_genome2_G2_G2: 10.03
  HiC_G1_UA_total: 203114
  HiC_percent_G1_UA_total: 25.12
  HiC_G1_UA: 101727
  HiC_UA_G1: 101387
  HiC_G2_UA_total: 186113
  HiC_percent_G2_UA_total: 23.02
  HiC_G2_UA: 92750
  HiC_UA_G2: 93363
  HiC_G1_G2_total: 8855
  HiC_percent_G1_G2_total: 1.10
  HiC_G1_G2: 4391
  HiC_G2_G1: 4464
  HiC_conflicting: 3366
  HiC_percent_conflicting: 0.42
...
FelixKrueger commented 4 years ago

YAML-wise this seems to be good enough for the moment.