| Input Reads | {NUMBER_READS} |
| Input Reference TRs | {NUMBER_REF_TRS} |
| Predicted VNTRs (span 2) | {NUMBER_REFS_VNTR_SPAN_N} |
| TRF executable | {PARAM_TRF_EXECUTABLE} |
| TRF parameters | {PARAM_TRF_PARAMS} |
| PROCLU parameters | {PARAM_PROCLU} |
| Min Support Required | {N_MIN_SUPPORT} |
| Min Flank Required | {MIN_FLANK_REQUIRED} |
| Max Flank Considered | {MAX_FLANK_CONSIDERED} |
| Output SQLite Database | {database} |
| Reads Input Folder | {FOLDER_FASTA} |
| Reads Profiles Output Folder | {FOLDER_PROFILES} |
| Reads Profiles Output Folder Clean | {FOLDER_PROFILES_CLEAN} |
| *Reference Folder | {FOLDER_REFERENCE} |
| Reference Seq File | {FILE_REFERENCE_SEQ} |
| Reference Profile File | {FILE_REFERENCE_LEB} |
| Input Reads | {NUMBER_READS} |
| Read TRs | {NUMBER_TRS_IN_READS} |
| Read TRs with pattern size >= 7 | {NUMBER_TRS_IN_READS_GE7} |
| Read TRs after cyclic redundancy | {NUMBER_TRS_IN_READS_AFTER_REDUND} |
| *Reference TRs after redundancy, filtering and pat >= 7 | {NUMBER_REF_TRS} |
| *Reference TRs after cyclic redundancy | {NUMBER_REFS_TRS_AFTER_REDUND} |
| Total clusters | {CLUST_NUMBER_OF_PROCLU_CLUSTERS} |
| Single Reference clusters | {NUMBER_REFS_SINGLE_REF_CLUSTER} |
| *Single Reference clusters with reads mapped | {NUMBER_REFS_SINGLE_REF_CLUSTER_WITH_READS_MAPPED} |
| *Single Reference clusters with no reads mapped | {NUMBER_REFS_SINGLE_REF_CLUSTER_WITH_NO_READS_MAPPED} |
| Total TRs clustered | {totReps}={CLUST_NUMBER_OF_REF_REPS_IN_CLUSTERS}+{CLUST_NUMBER_OF_READ_REPS_IN_CLUSTERS} |
| Reference TRs clustered | {CLUST_NUMBER_OF_REF_REPS_IN_CLUSTERS} |
| Read TR representatives clustered | {CLUST_NUMBER_OF_READ_REPS_IN_CLUSTERS} |
| Largest number of Reference TRs in cluster | {CLUST_LARGEST_NUMBER_OF_REFS_IN_PROCLU_CLUSTER} |
| Largest number of Read TRs in cluster | {CLUST_LARGEST_NUMBER_OF_TRS_IN_PROCLU_CLUSTER} |
| Largest cluster pattern range | {CLUST_LARGEST_PATRANGE_IN_PROCLU_CLUSTER}% |
| *Predicted Reference VNTRs with at least one read support | {CLUST_NUMBER_OF_REFS_WITH_PREDICTED_VNTR} |
| *Predicted Clusters with VNTRs with at least one read support | {CLUST_NUMBER_OF_CLUSTERS_WITH_PREDICTED_VNTR} |
| Predicted Reference VNTRs with at least two read support | {NUMBER_REFS_VNTR_SPAN_N} |
| *Read TR to Reference TR mappings by profile | {NUMBER_MAPPED} |
| *Read TR to Reference TR mappings by profile over profile score cutoff (some inferior scores removed) | {RANK_EDGES_OVERCUTOFF} |
| *Read TR to Reference TR mappings by profile removed: mapped to same ref from same read with lower profile score or lower id when tied score | {RANK_REMOVED_SAMEREF} |
| *Read TRs removed because PCR duplicate | {RANK_REMOVED_PCRDUP} |
| *Final Read TR to Reference TR mappings by profile | {NUMBER_RANK}: warning if {NUMBER_RANK}!={RANK_EDGES_OVERCUTOFF}-{RANK_REMOVED_SAMEREF}-{RANK_REMOVED_SAMESEQ}-{RANK_REMOVED_PCRDUP} |
| READ-REF PAIRS MEETING FLANKING CRITERIA (some inferior scores removed) | {RANKFLANK_EDGES_INSERTED} |
| RANKFLANK_REMOVED_NOT_TO_BEST_REF | {RANKFLANK_REMOVED_SAMEREF} |
| RANKFLANK_REMOVED_TRS_WHEN_CAME_FROM_SAME_READ | {RANKFLANK_REMOVED_SAMESEQ} |
| RANKFLANK_REMOVED_PCRDUP | {RANKFLANK_REMOVED_PCRDUP} |
| FINAL RANKFLANK ENTRIES | {NUMBER_RANKFLANK}: warning if {NUMBER_RANKFLANK}!={RANKFLANK_EDGES_INSERTED}-{RANKFLANK_REMOVED_SAMESEQ}-{RANKFLANK_REMOVED_SAMESEQ}-{RANKFLANK_REMOVED_PCRDUP} |
| *Intersection of Rank Profile and Rank Flank tables | {INTERSECT_RANK_AND_RANKFLANK_BEFORE_PCR} |
| *Intersection of Rank Profile and Rank Flank tables (after removing PCR duplicates) | {INTERSECT_RANK_AND_RANKFLANK} |
| *BBB (after removal of ties) | {BBB_WITH_MAP_DUPS} |
| *BBB (after removing far located refs map duplicates) | {BBB} |
| Step 0 (MySql DB Create) | {TIME_MYSQLCREATE} ({DATE_MYSQLCREATE}) |
| Step 1 (TRF) | {TIME_TRF} ({DATE_TRF}) |
| Step 2 (Renumbering) | {TIME_RENUMB} ({DATE_RENUMB}) |
| Step 3 (Cyc. Redund.) | {TIME_REDUND} ({DATE_REDUND}) |
| Step 4 (PROCLU) | {TIME_PROCLU} ({DATE_PROCLU}) |
| Step 5 (Join clusters) | {TIME_JOINCLUST} ({DATE_JOINCLUST}) |
| Step 8 (DB insert Read TRs) | {TIME_DB_INSERT_READS} ({DATE_DB_INSERT_READS}) |
| Step 9 (Write Flanks) | {TIME_WRITE_FLANKS} ({DATE_WRITE_FLANKS}) |
| Step 10 (Map Refs to Reads using Flanks) | {TIME_MAP_FLANKS} ({DATE_MAP_FLANKS}) |
| Step 12 (Map and Flank Rank information db insert) | {TIME_MAP_INSERT} ({DATE_MAP_INSERT}) |
| Step 13 (Calculate Ref to Read Profile Scores) | {TIME_EDGES} ({DATE_EDGES}) |
| Step 14 (Generating index files for PCRDUP step) | {TIME_INDEX_PCR} ({DATE_INDEX_PCR}) |
| Step 15 (Calculating PCR duplciates) | {TIME_PCR_DUP} ({DATE_PCR_DUP}) |
| Step 16 (Calculating mapped duplciates) | {TIME_MAP_DUP} ({DATE_MAP_DUP}) |
| Step 17 (VNTR prediction) | {TIME_VNTR_PREDICT} ({DATE_VNTR_PREDICT}) |
| Step 19 (Generate Reports) | {TIME_REPORTS} ({DATE_REPORTS}) |
| TOTAL | {total_time} |
