v1.0.4

yangao07 · Oct 6, 2020 · 681cee4 · 681cee4
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diff --git a/README.md b/README.md
@@ -8,12 +8,17 @@
 [![Build Status](https://img.shields.io/travis/yangao07/abPOA/master.svg?label=Master)](https://travis-ci.org/yangao07/abPOA)
 [![License](https://img.shields.io/badge/License-MIT-black.svg)](https://github.com/yangao07/abPOA/blob/master/LICENSE)
 <!-- [![PyPI](https://img.shields.io/pypi/v/pyabpoa.svg?style=flat)](https://pypi.python.org/pypi/pyabpoa) -->
+## Updates (v1.0.4)
+
+- Added read ID as head in MSA output: `-A`
+- Added GFA output: `-r3`/`-r4`
+- Added ambiguous strand mode: `-s`
 
 ## Getting started
 Download the [latest release](https://github.com/yangao07/abPOA/releases):
 ```
-wget https://github.com/yangao07/abPOA/releases/download/v1.0.3/abPOA-v1.0.3.tar.gz
-tar -zxvf abPOA-v1.0.3.tar.gz && cd abPOA-v1.0.3
+wget https://github.com/yangao07/abPOA/releases/download/v1.0.4/abPOA-v1.0.4.tar.gz
+tar -zxvf abPOA-v1.0.4.tar.gz && cd abPOA-v1.0.4
 ```
 Make from source and run with test data:
 ```
@@ -75,9 +80,9 @@ You can also build abPOA from source files.
 Make sure you have gcc (>=6.4.0) and zlib installed before compiling.
 It is recommended to download the [latest release](https://github.com/yangao07/abPOA/releases).
 ```
-wget https://github.com/yangao07/abPOA/releases/download/v1.0.3/abPOA-v1.0.3.tar.gz
-tar -zxvf abPOA-v1.0.3.tar.gz
-cd abPOA-v1.0.3; make
+wget https://github.com/yangao07/abPOA/releases/download/v1.0.4/abPOA-v1.0.4.tar.gz
+tar -zxvf abPOA-v1.0.4.tar.gz
+cd abPOA-v1.0.4; make
 ```
 Or, you can use `git clone` command to download the source code.
 This gives you the latest version of abPOA, which might be still under development.
@@ -89,8 +94,8 @@ cd abPOA; make
 ### <a name="binary"></a>Pre-built binary executable file for Linux/Unix 
 If you meet any compiling issue, please try the pre-built binary file:
 ```
-wget https://github.com/yangao07/abPOA/releases/download/v1.0.3/abPOA-v1.0.3_x64-linux.tar.gz
-tar -zxvf abPOA-v1.0.3_x64-linux.tar.gz
+wget https://github.com/yangao07/abPOA/releases/download/v1.0.4/abPOA-v1.0.4_x64-linux.tar.gz
+tar -zxvf abPOA-v1.0.4_x64-linux.tar.gz
 ```
 
 ## <a name="usage"></a>General usage

diff --git a/python/cabpoa.pxd b/python/cabpoa.pxd
@@ -43,6 +43,8 @@ cdef extern from "abpoa.h":
         uint64_t *graph_cigar
         int node_s, node_e, query_s, query_e # for local and  extension mode
         int n_aln_bases, n_matched_bases
+        uint32_t best_score
+        uint8_t is_rc
 
 
     ctypedef struct abpoa_para_t:
@@ -56,13 +58,16 @@ cdef extern from "abpoa.h":
         int simd_flag # available SIMD instruction
         # alignment mode
         uint8_t ret_cigar, rev_cigar, out_msa, out_msa_header, out_cons, out_gfa, is_diploid, use_read_ids # mode: 0: global, 1: local, 2: extend
+        uint8_t amb_strand
         char *out_pog
         int align_mode, gap_mode, cons_agrm
         double min_freq # for diploid data
+        char LogTable65536[65536]
+        char bit_table16[65536]
 
 
     ctypedef struct abpoa_node_t:
-        int node_id, index, rank
+        int node_id
         int in_edge_n, in_edge_m
         int *in_id
         int out_edge_n, out_edge_m
@@ -73,19 +78,19 @@ cdef extern from "abpoa.h":
         int read_ids_n # for diploid
         int aligned_node_n, aligned_node_m
         int *aligned_node_id # mismatch; aligned node will have same rank
-        int heaviest_weight, heaviest_out_id # for consensus
         uint8_t base # 0~m
 
     ctypedef struct abpoa_graph_t:
         abpoa_node_t *node
         int node_n, node_m, index_rank_m
         int *index_to_node_id
         int *node_id_to_index 
-        int *node_id_to_min_rank
-        int *node_id_to_max_rank
+        int *node_id_to_max_pos_left
+        int *node_id_to_max_pos_right
         int *node_id_to_max_remain
         int *node_id_to_msa_rank
         uint8_t is_topological_sorted, is_called_cons, is_set_msa_rank
+        double cal_R_time
 
     ctypedef struct abpoa_simd_matrix_t:
         pass
@@ -105,7 +110,7 @@ cdef extern from "abpoa.h":
     void abpoa_free(abpoa_t *ab, abpoa_para_t *abpt)
 
     # do msa for a set of input sequences
-    int abpoa_msa(abpoa_t *ab, abpoa_para_t *abpt, int n_seqs, char **seq_names, int *seq_lens, uint8_t **seqs, FILE *out_fp, uint8_t ***cons_seq, int **cons_l, int *cons_n, uint8_t ***msa_seq, int *msa_l)
+    int abpoa_msa(abpoa_t *ab, abpoa_para_t *abpt, int n_seqs, char **seq_names, int *seq_lens, uint8_t **seqs, FILE *out_fp, uint8_t ***cons_seq, uint8_t ***cons_cov, int **cons_l, int *cons_n, uint8_t ***msa_seq, int *msa_l)
 
     # clean alignment graph
     void abpoa_reset_graph(abpoa_t *ab, abpoa_para_t *abpt, int qlen)
@@ -115,8 +120,8 @@ cdef extern from "abpoa.h":
 
     # add an alignment to a graph
     int abpoa_add_graph_node(abpoa_graph_t *abg, uint8_t base)
-    void abpoa_add_graph_edge(abpoa_graph_t *abg, int from_id, int to_id, int check_edge, uint8_t add_read_id, int read_id, int read_ids_n)
-    int abpoa_add_graph_alignment(abpoa_t *ab, abpoa_para_t *abpt, uint8_t *query, int qlen, int n_cigar, uint64_t *abpoa_cigar, int read_id, int tot_read_n)
+    void abpoa_add_graph_edge(abpoa_graph_t *abg, int from_id, int to_id, int check_edge, int w, uint8_t add_read_id, int read_id, int read_ids_n)
+    int abpoa_add_graph_alignment(abpoa_t *ab, abpoa_para_t *abpt, uint8_t *query, int qlen, abpoa_res_t res, int read_id, int tot_read_n)
     void abpoa_topological_sort(abpoa_graph_t *abg, abpoa_para_t *abpt)
 
     # generate consensus sequence from graph
@@ -129,10 +134,10 @@ cdef extern from "abpoa.h":
     #     Note: cons_seq and cons_l need to be freed by user.
     int abpoa_generate_consensus(abpoa_t *ab, abpoa_para_t *abpt, int seq_n, FILE *out_fp, uint8_t ***cons_seq, int ***cons_cov, int **cons_l, int *cons_n)
     # generate column multiple sequence alignment from graph
-    void abpoa_generate_rc_msa(abpoa_t *ab, abpoa_para_t *abpt, char **seq_names, int seq_n, FILE *out_fp, uint8_t ***msa_seq, int *msa_l)
+    void abpoa_generate_rc_msa(abpoa_t *ab, abpoa_para_t *abpt, char **seq_names, uint8_t *is_rc, int seq_n, FILE *out_fp, uint8_t ***msa_seq, int *msa_l)
 
     # generate full graph in GFA format
-    void abpoa_generate_gfa(abpoa_t *ab, abpoa_para_t *abpt, char **seq_names, int seq_n, FILE *out_fp)
+    void abpoa_generate_gfa(abpoa_t *ab, abpoa_para_t *abpt, char **seq_names, uint8_t *is_rc, int seq_n, FILE *out_fp)
 
     # generate DOT graph plot 
     int abpoa_dump_pog(abpoa_t *ab, abpoa_para_t *abpt)
diff --git a/python/example.py b/python/example.py
@@ -35,7 +35,7 @@
 #@parameters of msa
 #seqs: multiple sequences
 out_cons=True # generate consensus sequence, set as False to disable
-out_msa=True  # generate row-column multiple sequence alignment, set as False to disable
+out_msa=True # generate row-column multiple sequence alignment, set as False to disable
 out_pog="example.png" # generate plot of alignment graph, set None to disable
 
 # multiple sequence alignment for 'seqs'

diff --git a/python/pyabpoa.pyx b/python/pyabpoa.pyx
@@ -143,9 +143,10 @@ cdef class msa_aligner:
             for i in range(seq_l):
                 bseq[i] = self.seq_nt4_dict[seq[i]]
             res.n_cigar = 0
+            res.is_rc = 0
             abpoa_align_sequence_to_graph(self.ab, &self.abpt, bseq, seq_l, &res)
 
-            abpoa_add_graph_alignment(self.ab, &self.abpt, bseq, seq_l, res.n_cigar, res.graph_cigar, read_i, seq_n)
+            abpoa_add_graph_alignment(self.ab, &self.abpt, bseq, seq_l, res, read_i, seq_n)
             free(bseq)
             if res.n_cigar: free(res.graph_cigar)
 
@@ -164,7 +165,7 @@ cdef class msa_aligner:
                 free(cons_seq)
                 free(cons_len)
         if self.abpt.out_msa:
-            abpoa_generate_rc_msa(self.ab, &self.abpt, NULL, seq_n, NULL, &msa_seq, &msa_l)
+            abpoa_generate_rc_msa(self.ab, &self.abpt, NULL, NULL, seq_n, NULL, &msa_seq, &msa_l)
             for i in range(seq_n):
                 msa_seq1 = ''
                 for c in msa_seq[i][:msa_l]:

diff --git a/src/abpoa_graph.c b/src/abpoa_graph.c
@@ -452,7 +452,7 @@ int abpoa_store_consensus(abpoa_graph_t *abg, int src_id, int sink_id, uint8_t *
     (*cons_seq)[0] = (uint8_t*)_err_malloc(sizeof(uint8_t) * abg->node_n);
     int id = abg->node[src_id].max_out_id, i = 0;
     while (id != sink_id) {
-        (*cons_seq)[0][i++] = "ACGTN"[abg->node[id].base];
+        (*cons_seq)[0][i++] = abg->node[id].base;
         id = abg->node[id].max_out_id;
     }
     (*cons_l)[0] = i;