Suboptimal alignment

[sebschmi]

Before:

cargo run --release -- align --alignment-method a-star-chain-ts -c test_files/config/chainalignn -p test_files/twin_ari_email_244.fa --log-level debug -k 7 --skip-characters N- --max-chaining-successors 1 --chaining-closed-list special --chaining-open-list linear-heap
    Blocking waiting for file lock on build directory
    Finished `release` profile [optimized + debuginfo] target(s) in 1m 46s
     Running `target/release/tsalign align --alignment-method a-star-chain-ts -c test_files/config/chainalignn -p test_files/twin_ari_email_244.fa --log-level debug -k 7 --skip-characters N- --max-chaining-successors 1 --chaining-closed-list special --chaining-open-list linear-heap`
10:44:02 [INFO] Loading pair file "test_files/twin_ari_email_244.fa"
10:44:02 [DEBUG] (1) tsalign::align::fasta_parser: Parsing fasta file "test_files/twin_ari_email_244.fa"
10:44:02 [DEBUG] (1) tsalign::align: Choosing alignment method...
10:44:02 [INFO] Loading alignment config directory "test_files/config/chainalignn"
10:44:02 [WARN] No cache directory specified, dropping files into current working directory.
10:44:02 [DEBUG] (1) tsalign::align::a_star_chain_ts: Using max_n = 2048
10:44:02 [INFO] Using k = 7
10:44:02 [DEBUG] (1) tsalign::align::a_star_chain_ts: Using cost_hash = 5af62ef97ff186287afd4ba475a699cabf11038c
10:44:02 [INFO] Loading preprocessed data from cache at "5af62ef97ff186287afd4ba475a699cabf11038c-7-2048.tsc"
10:44:02 [DEBUG] (1) lib_ts_chainalign: Reference sequence: GGGAGCGTGGCAGAGGGAATGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAATGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCATGGCTGACATTGAGGAAGGAGCTGGCAGAGGGAATGATGGCCGTGGTGACACTGAAGAGGGAGCGTGGCAGAGGGAATGATGGCCATGGTGAAACTGAGGAGGGAGCGTGGCAGAGGGAATGATGGCCGTGGTGATATTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCATGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCATGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCATGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCATGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCATGGCTGACATTGAGGAGGGAGCTGGCAGAGGGAACGATGGCCATGGCTGACATTGAGGAGGGAGCGTGGCAGAAGGAACGATGGCCATGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGCTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGCTGACAC
10:44:02 [DEBUG] (1) lib_ts_chainalign: Query sequence: GGGAGCGTGGCAGAGGGAATGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAATGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCATGGCTGACATTGAGGAAGGAGCTGGCAGAGGGAATGATGGCCGTGGTGACACTGAAGAGGGAGCGTGGCAGAGGGAATGATGGCCATGGTGAAACTGAGGAGGGAGCGTGGCAGAGGGAATGATGGCCGTGGTGATATTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCATGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCATGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCATGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCATGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCATGGCTGACATTGAGGAGGGAGCTGGCAGAGGGAACGATGGCCGTGGTGACATTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCATGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCATGGTGACACTGAGGAGGGAGCGTGGCAGGTGGCAGAGGGAACGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGCTGACACTGAGGAGGGAGCGTGGCAGAGGGAACGATGGCCGTGGCTGACAC
10:44:02 [INFO] Aligning on subsequence R: 0..1072; Q: 0..1121
10:44:02 [INFO] Found 21075 anchors (20247 + 216 + 207 + 207 + 198) in 2ms
10:44:05 [DEBUG] (1) lib_ts_chainalign::chaining_cost_function: Initialising chaining cost function took 3039ms
11:42:02 [DEBUG] (1) lib_ts_chainalign::chain_align: Computed 4378 chains
11:42:02 [DEBUG] (1) lib_ts_chainalign::chain_align: Chaining took 3360.3s
11:42:02 [DEBUG] (1) lib_ts_chainalign::chain_align: Evaluation took 117.1s
11:42:02 [DEBUG] (1) lib_ts_chainalign::chain_align: Chaining opened nodes: 43305054832
11:42:02 [DEBUG] (1) lib_ts_chainalign::chain_align: Chaining suboptimal openend nodes: 32191290476 (74% of opened nodes)
11:42:02 [DEBUG] (1) lib_ts_chainalign::chain_align: Chaining closed nodes: 875829906
11:42:02 [DEBUG] (1) lib_ts_chainalign::chain_align: Total chain gaps: 1347129
11:42:02 [DEBUG] (1) lib_ts_chainalign::chain_align: Total chain gap fillings: 11836 (0.01x total gaps, 0% redundant)
11:42:02 [DEBUG] (1) lib_ts_chainalign::chain_align: Evaluating final chain
11:42:02 [INFO] Finished aligning
CIGAR: 365M[TSRRR:[-]:[-]:181:8M:180]36M[TSQRR:[-]:[-]:92:7M:137]20M7I506M
Reached target with cost 13
Reference offset: 0
Query offset: 0
Cost per base: 0.01
Opened nodes: 0
Closed nodes: 0
Suboptimal openend nodes: 0
Suboptimal openend nodes per optimal opened node: 0.00
Duration: 3477.48s

After:

Reached target with cost 15