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ruanjue / smartdenovo

Ultra-fast de novo assembler using long noisy reads
GNU General Public License v3.0
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failed to `make wtcorr ` #32

Closed zhangrengang closed 5 years ago

zhangrengang commented 5 years ago

I want to test wtcorr. However, it failed to compile:

$ make wtcorr
gcc -W -Wall -O4 -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -mpopcnt -mssse3 -o wtcorr wtcorr.c file_reader.c -lm -lpthread
wtcorr.c:388:1: error: invalid suffix "hashcode" on integer constant
wtcorr.c:388:1: error: invalid suffix "hashcode" on integer constant
wtcorr.c:388:1: error: invalid suffix "hashcode" on integer constant
wtcorr.c:388:1: error: invalid suffix "hashcode" on integer constant
wtcorr.c:388:1: error: invalid suffix "hashcode" on integer constant
wtcorr.c:388:1: error: invalid suffix "hashcode" on integer constant
wtcorr.c:422:1: warning: "E" redefined
wtcorr.c:385:1: warning: this is the location of the previous definition
wtcorr.c: In function 'get_dphash':
wtcorr.c:425: error: 'gdpv' undeclared (first use in this function)
wtcorr.c:425: error: (Each undeclared identifier is reported only once
wtcorr.c:425: error: for each function it appears in.)
wtcorr.c:425: error: expected expression before ')' token
wtcorr.c:425: error: expected expression before ')' token
wtcorr.c:425: error: expected expression before ')' token
wtcorr.c: In function 'prepare_dphash':
wtcorr.c:425: error: 'gdpv' undeclared (first use in this function)
wtcorr.c:425: error: expected expression before ')' token
wtcorr.c:425: error: expected expression before ')' token
wtcorr.c:425: error: expected expression before ')' token
wtcorr.c: In function 'exists_dphash':
wtcorr.c:425: error: 'gdpv' undeclared (first use in this function)
wtcorr.c:425: error: expected expression before ')' token
wtcorr.c:425: error: expected expression before ')' token
wtcorr.c:425: error: expected expression before ')' token
wtcorr.c: In function 'add_dphash':
wtcorr.c:425: error: 'gdpv' undeclared (first use in this function)
wtcorr.c:425: error: expected expression before ')' token
wtcorr.c:425: error: expected expression before ')' token
wtcorr.c:425: error: expected expression before ')' token
wtcorr.c: In function 'remove_dphash':
wtcorr.c:425: error: 'gdpv' undeclared (first use in this function)
wtcorr.c:425: error: expected expression before ')' token
wtcorr.c:425: error: expected expression before ')' token
wtcorr.c:425: error: expected expression before ')' token
wtcorr.c: In function 'encap_dphash':
wtcorr.c:425: error: 'gdpv' undeclared (first use in this function)
wtcorr.c:425: error: expected expression before ')' token
wtcorr.c: In function 'last_base_dp_kmer':
wtcorr.c:554: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c:554: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c: In function 'trace_aln_paths':
wtcorr.c:565: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:565: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c: In function 'count_covered_qmers':
wtcorr.c:584: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:584: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c: In function 'call_correct_seq':
wtcorr.c:624: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:624: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:636: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c:636: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c:644: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:651: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:651: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:659: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c:659: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c:681: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c: In function 'init_bf_kmer_dbgaln':
wtcorr.c:689: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c:689: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c: In function 'print_dp_kmers':
wtcorr.c:724: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c:724: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c: In function 'dbg_aln_core':
wtcorr.c:757: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:757: error: 'dbg_aligner' has no member named 'qmaxs'
wtcorr.c:757: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:772: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:776: error: 'dbg_aligner' has no member named 'smin'
wtcorr.c:782: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:782: error: 'dbg_aligner' has no member named 'qtop'
wtcorr.c:784: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:784: error: 'dbg_aligner' has no member named 'qtop'
wtcorr.c:785: error: 'dbg_aligner' has no member named 'qtop'
wtcorr.c:785: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:788: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:788: error: 'dbg_aligner' has no member named 'qtop'
wtcorr.c:793: error: 'dbg_aligner' has no member named 'qmaxs'
wtcorr.c:793: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:795: error: 'dbg_aligner' has no member named 'qmaxs'
wtcorr.c:795: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:796: error: 'dbg_aligner' has no member named 'qmaxs'
wtcorr.c:796: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:804: warning: implicit declaration of function 'process_cached_dps_dbgaln'
wtcorr.c:818: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c:822: error: 'dbg_dp_t' has no member named 'fw_idx'
wtcorr.c:823: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c:823: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c:826: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:829: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:834: error: 'dc' undeclared (first use in this function)
wtcorr.c:834: warning: implicit declaration of function 'prepare_dbgcachehash'
wtcorr.c:834: error: 'dbg_aligner' has no member named 'gcache'
wtcorr.c:834: error: 'dbg_cache_t' undeclared (first use in this function)
wtcorr.c:834: error: expected ')' before '{' token
wtcorr.c:835: error: 'dc_exists' undeclared (first use in this function)
wtcorr.c:837: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c:838: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:854: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c:868: error: 'dbg_dp_t' has no member named 'aux1'
wtcorr.c:871: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c:874: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:874: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:875: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c:881: error: 'dbg_dp_t' has no member named 'link'
wtcorr.c:895: error: 'dbg_dp_t' has no member named 'aux1'
wtcorr.c:897: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c:899: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:899: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:900: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c:906: error: 'dbg_dp_t' has no member named 'link'
wtcorr.c:918: error: 'dbg_dp_t' has no member named 'aux1'
wtcorr.c:921: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:921: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:922: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c:922: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c:928: error: 'dbg_dp_t' has no member named 'link'
wtcorr.c:752: warning: unused variable 'qpos'
wtcorr.c:752: warning: unused variable 'found'
wtcorr.c:752: warning: unused variable 'kc_exists'
wtcorr.c:750: warning: unused variable 'path'
wtcorr.c:750: warning: unused variable 'pidx'
wtcorr.c:750: warning: unused variable 'didx'
wtcorr.c:749: warning: unused variable 'BR'
wtcorr.c:749: warning: unused variable 'BK'
wtcorr.c:749: warning: unused variable 'bk'
wtcorr.c:747: warning: unused variable 'kc'
wtcorr.c:746: warning: unused variable 'dp1'
wtcorr.c: In function 'dbg_aln':
wtcorr.c:940: warning: implicit declaration of function 'clear_dbgcachehash'
wtcorr.c:940: error: 'dbg_aligner' has no member named 'gcache'
wtcorr.c:947: error: 'dbg_aligner' has no member named 'qmaxs'
wtcorr.c:948: error: 'dbg_aligner' has no member named 'qmaxs'
wtcorr.c:972: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:973: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c:998: error: 'dbg_dp_t' has no member named 'aux1'
wtcorr.c:999: error: 'dbg_dp_t' has no member named 'aux2'
wtcorr.c:1001: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c:1001: error: 'dbg_dp_t' has no member named 'k'
wtcorr.c:1005: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:1005: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:1005: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:1007: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:1007: error: 'dbg_aligner' has no member named 'qmaxs'
wtcorr.c:1010: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:1011: error: 'dbg_aligner' has no member named 'qtop'
wtcorr.c:1011: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:1012: error: 'dbg_aligner' has no member named 'last_cached_pos'
wtcorr.c:1044: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:1045: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:1045: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:1045: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:1045: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:1063: error: 'dbg_dp_t' has no member named 'mat'
wtcorr.c:1080: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:1080: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c: In function 'main':
wtcorr.c:1399: error: 'DBG_MAX_BT_IDX' undeclared (first use in this function)
wtcorr.c:1423: error: 'dbg_aligner' has no member named 'smin'
wtcorr.c:1450: error: 'dbg_dp_t' has no member named 'qpos'
wtcorr.c:1456: error: 'dbg_dp_t' has no member named 'qpos'
make: *** [wtcorr] Error 1

How to do with it?

ruanjue commented 5 years ago

wtcorr builds a DBG from short reads to correct long reads. It was implemented in very old version, and lost in updates. Sorry, I cannot spare enough time to revive it.