huanglangwen
commented
4 years ago Interestingly, eval.py gives no diff if ind is fixed (at 0?), while there are diffs when ind = maxind(traceback).
Closed huanglangwen closed 4 years ago
huanglangwen
commented
4 years ago Interestingly, eval.py gives no diff if ind is fixed (at 0?), while there are diffs when ind = maxind(traceback).
huanglangwen
commented
4 years ago PS C:\Users\huang\Documents\programs\parallel-genomeseq\py> ipython eval.py sw_solve_small
No diffs
PS C:\Users\huang\Documents\programs\parallel-genomeseq\py> ipython eval.py sw_solve_small
12/1170 alignments different from ground truth
May be caused by cost function. There is often no unique correct solution.
QNAME SEQ POS pos_pred score delta_pos
index
90 22_5K-1080 CGTTGAAGTTGGGGTCTTTCCCACCACATGGCACCACCCCAAGGAG... 1036 1037 123 1
116 22_5K-1054 TTAATTTTGAGACACGGAGTCTCACTTGGTCGCCCAGGCTGGAGTG... 1616 1619 121 3
117 22_5K-1054 CCAATTTGTTATTTAAAAAAAATTTTAATTCTTTTTTAGAGACAGG... 1907 1910 121 3
354 22_5K-816 GGACAGCTATAGTCCCAGCTACTTGAAAGTCTGAAGCAGGAGATTC... 2898 2900 122 2
376 22_5K-794 AGGCAGTCAGAATTGGAGCCAGCCTGCCCCTCAGCTGGGAGCCTGG... 3429 3431 122 2
395 22_5K-776 TATTTGAGACACGGAGTCTCACTTGGTCGCCCAGGCTGGAGTGCAG... 1619 1620 123 1
400 22_5K-770 AACGTGCCGGAATTACAGGCATGAGCCACTGCACCCAGCCCGCCTG... 4171 4173 122 2
439 22_5K-732 ACCGAGCAAGACATCTTCTGAAAAATAATACAGTACCTATGTGATA... 3009 3011 122 2
591 22_5K-580 TGGTTCAACATTTCGGTAATTCTTATTGCATTTCAATAATTCTTAT... 4642 4643 118 1
934 22_5K-236 AAAGATACAAAAATTAGCTGGGCATGGTGGTGCTCGCCTGTAGTCC... 2230 2233 121 3
942 22_5K-228 AGGCCATGGGACAGATGGGGGAAGGGTACAGGGCACCTGGGAAGTA... 2557 2560 116 3
1150 22_5K-20 CTCTTGAGTATATATTTAGTTCAACGTAAAACCATCCATCTCGGCC... 404 405 118 1
This would simplify a ton of code, and it's a lot safer by saving manual memory management and auto boundary check.
BTW, you don't have to install Eigen, cmake does everything for you :)