1. gmapR
  2. src
  3. gstruct
  4. src
  5. bamread.h
Browse code

update GSTRUCT source code

Michael Lawrence authored on 22/05/2019 19:39:45
Showing 1 changed files
src/gstruct/src/bamread.h
History View file @ 7cb8750
... ... 
@@ -1,4 +1,4 @@
1 
-/* $Id: bamread.h 198589 2016-10-01 04:22:06Z twu $ */
1 
+/* $Id: bamread.h 219284 2019-05-21 01:02:18Z twu $ */
2 2 
 #ifndef BAMREAD_INCLUDED
3 3 
 #define BAMREAD_INCLUDED
4 4 
 /* Cannot use bool, since it appears to conflict with samtools */
... ... 
@@ -86,6 +86,8 @@ extern Genomicpos_T
86 86 
 Bamline_mate_chrpos_low (Bamline_T this);
87 87 
 extern int
88 88 
 Bamline_insert_length (Bamline_T this);
89 
+extern int
90 
+Bamline_nmult (Bamline_T this);
89 91
90 92 
 extern char *
91 93 
 Bamline_cigar_string (Bamline_T this);
... ... 
@@ -98,6 +100,8 @@ extern Intlist_T
98 100 
 Bamline_diffcigar (int *min_overhang, Uintlist_T *npositions, Uintlist_T *chrpositions, Bamline_T this);
99 101 
 extern int
100 102 
 Bamline_cigar_querylength (Bamline_T this);
103 
+extern int
104 
+Bamline_cigar_outer_softclip_length (Bamline_T this);
101 105 
 extern void
102 106 
 Bamread_print_cigar (FILE *fp, Bamline_T this);
103 107 
 extern char *
... ... 
@@ -116,6 +120,8 @@ extern bool
116 120 
 Bamline_terminalp (Bamline_T this);
117 121 
 extern char *
118 122 
 Bamline_read_group (Bamline_T this);
123 
+extern bool
124 
+Bamline_exon_overlap_p (Bamline_T this, Genomicpos_T chrstart, Genomicpos_T chrend);
119 125 
 extern void
120 126 
 Bamline_print (FILE *fp, Bamline_T this, unsigned int newflag, int quality_score_adj);
121 127 
 extern void
Browse code

update to latest GSTRUCT

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@123972 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 14/11/2016 21:54:30
Showing 1 changed files
src/gstruct/src/bamread.h
History View file @ 55d77a1
... ... 
@@ -1,4 +1,4 @@
1 
-/* $Id: bamread.h 178960 2015-11-16 19:52:26Z twu $ */
1 
+/* $Id: bamread.h 198589 2016-10-01 04:22:06Z twu $ */
2 2 
 #ifndef BAMREAD_INCLUDED
3 3 
 #define BAMREAD_INCLUDED
4 4 
 /* Cannot use bool, since it appears to conflict with samtools */
... ... 
@@ -52,6 +52,8 @@ extern char *
52 52 
 Bamline_acc (Bamline_T this);
53 53 
 extern unsigned int
54 54 
 Bamline_flag (Bamline_T this);
55 
+extern bool
56 
+Bamline_plusp (Bamline_T this);
55 57 
 extern int
56 58 
 Bamline_concordantp (Bamline_T this);
57 59 
 extern int
... ... 
@@ -68,6 +70,8 @@ extern bool
68 70 
 Bamline_good_unique_p (Bamline_T this);
69 71 
 extern bool
70 72 
 Bamline_perfect_match_p (Bamline_T this);
73 
+extern bool
74 
+Bamline_microinv_p (Bamline_T this);
71 75 
 extern int
72 76 
 Bamline_mapq (Bamline_T this);
73 77 
 extern char *
... ... 
@@ -82,10 +86,14 @@ extern Genomicpos_T
82 86 
 Bamline_mate_chrpos_low (Bamline_T this);
83 87 
 extern int
84 88 
 Bamline_insert_length (Bamline_T this);
89 
+
90 
+extern char *
91 
+Bamline_cigar_string (Bamline_T this);
85 92 
 extern Intlist_T
86 93 
 Bamline_cigar_types (Bamline_T this);
87 94 
 extern Uintlist_T
88 95 
 Bamline_cigar_npositions (Bamline_T this);
96 
+
89 97 
 extern Intlist_T
90 98 
 Bamline_diffcigar (int *min_overhang, Uintlist_T *npositions, Uintlist_T *chrpositions, Bamline_T this);
91 99 
 extern int
Browse code

add raw total count statistic to tallies (everything else now qual filtered)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@110891 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 24/11/2015 22:19:59
Showing 1 changed files
src/gstruct/src/bamread.h
History View file @ 5659f09
... ... 
@@ -1,4 +1,4 @@
1 
-/* $Id: bamread.h 160725 2015-03-11 16:45:17Z twu $ */
1 
+/* $Id: bamread.h 178960 2015-11-16 19:52:26Z twu $ */
2 2 
 #ifndef BAMREAD_INCLUDED
3 3 
 #define BAMREAD_INCLUDED
4 4 
 /* Cannot use bool, since it appears to conflict with samtools */
... ... 
@@ -61,6 +61,8 @@ Bamline_paired_read_p (Bamline_T this);
61 61 
 extern int
62 62 
 Bamline_firstend_p (Bamline_T this);
63 63 
 extern int
64 
+Bamline_hiti (Bamline_T this);
65 
+extern int
64 66 
 Bamline_nhits (Bamline_T this);
65 67 
 extern bool
66 68 
 Bamline_good_unique_p (Bamline_T this);
... ... 
@@ -169,7 +171,7 @@ Bamstore_new (Genomicpos_T chrpos);
169 171
170 172 
 extern Bamline_T
171 173 
 Bamstore_get (Table_T bamstore_chrtable, char *chr, Genomicpos_T low, char *acc,
172 
-	      Genomicpos_T mate_low);
174 
+	      Genomicpos_T mate_low, int hiti);
173 175
174 176 
 extern void
175 177 
 Bamstore_add_at_low (Table_T bamstore_chrtable, char *chr, Genomicpos_T low,
... ... 
@@ -191,9 +193,16 @@ extern Genomicpos_T
191 193 
 Bampair_chrpos_low (Bampair_T this);
192 194 
 extern Genomicpos_T
193 195 
 Bampair_chrpos_high (Bampair_T this);
196 
+extern Genomicpos_T
197 
+Bampair_chrpos_low_noclip (Bampair_T this);
198 
+extern Genomicpos_T
199 
+Bampair_chrpos_high_noclip (Bampair_T this);
200 
+
194 201 
 extern int
195 202 
 Bampair_level (Bampair_T this);
196 203 
 extern bool
204 
+Bampair_plusp (Bampair_T this);
205 
+extern bool
197 206 
 Bampair_good_unique_p (Bampair_T this);
198 207 
 extern bool
199 208 
 Bampair_uniquep (Bampair_T this);
... ... 
@@ -205,7 +214,9 @@ Bampair_free (Bampair_T *old);
205 214 
 extern void
206 215 
 Bampair_print (FILE *fp, Bampair_T this, int quality_score_adj);
207 216 
 extern void
208 
-Bampair_details (Uintlist_T *chrpos_lows, Uintlist_T *chrpos_highs,
217 
+Bampair_details (Uintlist_T *chrpos_first_lows, Uintlist_T *chrpos_first_highs,
218 
+		 Uintlist_T *chrpos_second_lows, Uintlist_T *chrpos_second_highs,
219 
+		 Uintlist_T *chrpos_overlap_lows, Uintlist_T *chrpos_overlap_highs,
209 220 
 		 Uintlist_T *splice_lows, Uintlist_T *splice_highs, Intlist_T *splice_signs,
210 221 
 		 Bampair_T this);
211 222
Browse code

resurrect improvements that we reverted before the April release, expect breakage for a while

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@110039 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 28/10/2015 18:51:00
Showing 1 changed files
src/gstruct/src/bamread.h
History View file @ 8418591
... ... 
@@ -1,4 +1,4 @@
1 
-/* $Id: bamread.h 141010 2014-07-09 16:34:11Z twu $ */
1 
+/* $Id: bamread.h 160725 2015-03-11 16:45:17Z twu $ */
2 2 
 #ifndef BAMREAD_INCLUDED
3 3 
 #define BAMREAD_INCLUDED
4 4 
 /* Cannot use bool, since it appears to conflict with samtools */
... ... 
@@ -43,8 +43,8 @@ extern int
43 43 
 Bamread_next_line (T this, char **acc, unsigned int *flag, int *mapq, char **chr, Genomicpos_T *chrpos,
44 44 
 		   char **mate_chr, Genomicpos_T *mate_chrpos,
45 45 
 		   Intlist_T *cigartypes, Uintlist_T *cigarlengths, int *cigarlength,
46 
-		   int *readlength, char **read, char **quality_string, char **read_group,
47 
-		   bool *terminalp);
46 
+		   int *readlength, char **read, char **quality_string, char **hardclip, char **hardclip_quality,
47 
+		   char **read_group, bool *terminalp);
48 48
49 49 
 typedef struct Bamline_T *Bamline_T;
50 50
... ... 
@@ -85,7 +85,7 @@ Bamline_cigar_types (Bamline_T this);
85 85 
 extern Uintlist_T
86 86 
 Bamline_cigar_npositions (Bamline_T this);
87 87 
 extern Intlist_T
88 
-Bamline_diffcigar (Uintlist_T *npositions, Uintlist_T *chrpositions, Bamline_T this);
88 
+Bamline_diffcigar (int *min_overhang, Uintlist_T *npositions, Uintlist_T *chrpositions, Bamline_T this);
89 89 
 extern int
90 90 
 Bamline_cigar_querylength (Bamline_T this);
91 91 
 extern void
... ... 
@@ -98,6 +98,10 @@ extern char *
98 98 
 Bamline_read (Bamline_T this);
99 99 
 extern char *
100 100 
 Bamline_quality_string (Bamline_T this);
101 
+extern char *
102 
+Bamline_hardclip (Bamline_T this);
103 
+extern char *
104 
+Bamline_hardclip_quality (Bamline_T this);
101 105 
 extern bool
102 106 
 Bamline_terminalp (Bamline_T this);
103 107 
 extern char *
... ... 
@@ -111,6 +115,8 @@ extern void
111 115 
 Bamline_print_new_mate (FILE *fp, Bamline_T this, char *mate_chr, Genomicpos_T mate_chrpos_low,
112 116 
 			int insert_length);
113 117
118 
+extern int
119 
+Bamline_nm (Bamline_T this);
114 120 
 extern char
115 121 
 Bamline_splice_strand (Bamline_T this);
116 122
... ... 
@@ -143,6 +149,12 @@ Bamread_next_bamline_set (int *nlines, Bamline_T *prev_bamline,
143 149 
 			  bool need_unique_p, bool need_primary_p, bool ignore_duplicates_p,
144 150 
 			  bool need_concordant_p);
145 151
152 
+extern Bamline_T **
153 
+Bamread_block (int **nlines, Genomicpos_T chrstart, Genomicpos_T chrend,
154 
+	       T this, char *desired_read_group, int minimum_mapq, int good_unique_mapq, int maximum_nhits,
155 
+	       bool need_unique_p, bool need_primary_p, bool ignore_duplicates_p,
156 
+	       bool need_concordant_p);
157 
+
146 158 
 extern Bamline_T
147 159 
 Bamread_get_acc (T this, char *desired_chr, Genomicpos_T desired_chrpos, char *desired_acc);
148 160
... ... 
@@ -169,6 +181,8 @@ Bamstore_table_free (Uinttable_T *bamstore_table);
169 181
170 182 
 typedef struct Bampair_T *Bampair_T;
171 183
184 
+extern char *
185 
+Bampair_acc (Bampair_T this);
172 186 
 extern Bamline_T
173 187 
 Bampair_bamline_low (Bampair_T this);
174 188 
 extern Bamline_T
Browse code

Reverted to r101133, along with NAMESPACE fixes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@102487 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 14/04/2015 21:40:44
Showing 1 changed files
src/gstruct/src/bamread.h
History View file @ d5ed124
... ... 
@@ -1,4 +1,4 @@
1 
-/* $Id: bamread.h 160725 2015-03-11 16:45:17Z twu $ */
1 
+/* $Id: bamread.h 141010 2014-07-09 16:34:11Z twu $ */
2 2 
 #ifndef BAMREAD_INCLUDED
3 3 
 #define BAMREAD_INCLUDED
4 4 
 /* Cannot use bool, since it appears to conflict with samtools */
... ... 
@@ -43,8 +43,8 @@ extern int
43 43 
 Bamread_next_line (T this, char **acc, unsigned int *flag, int *mapq, char **chr, Genomicpos_T *chrpos,
44 44 
 		   char **mate_chr, Genomicpos_T *mate_chrpos,
45 45 
 		   Intlist_T *cigartypes, Uintlist_T *cigarlengths, int *cigarlength,
46 
-		   int *readlength, char **read, char **quality_string, char **hardclip, char **hardclip_quality,
47 
-		   char **read_group, bool *terminalp);
46 
+		   int *readlength, char **read, char **quality_string, char **read_group,
47 
+		   bool *terminalp);
48 48
49 49 
 typedef struct Bamline_T *Bamline_T;
50 50
... ... 
@@ -85,7 +85,7 @@ Bamline_cigar_types (Bamline_T this);
85 85 
 extern Uintlist_T
86 86 
 Bamline_cigar_npositions (Bamline_T this);
87 87 
 extern Intlist_T
88 
-Bamline_diffcigar (int *min_overhang, Uintlist_T *npositions, Uintlist_T *chrpositions, Bamline_T this);
88 
+Bamline_diffcigar (Uintlist_T *npositions, Uintlist_T *chrpositions, Bamline_T this);
89 89 
 extern int
90 90 
 Bamline_cigar_querylength (Bamline_T this);
91 91 
 extern void
... ... 
@@ -98,10 +98,6 @@ extern char *
98 98 
 Bamline_read (Bamline_T this);
99 99 
 extern char *
100 100 
 Bamline_quality_string (Bamline_T this);
101 
-extern char *
102 
-Bamline_hardclip (Bamline_T this);
103 
-extern char *
104 
-Bamline_hardclip_quality (Bamline_T this);
105 101 
 extern bool
106 102 
 Bamline_terminalp (Bamline_T this);
107 103 
 extern char *
... ... 
@@ -115,8 +111,6 @@ extern void
115 111 
 Bamline_print_new_mate (FILE *fp, Bamline_T this, char *mate_chr, Genomicpos_T mate_chrpos_low,
116 112 
 			int insert_length);
117 113
118 
-extern int
119 
-Bamline_nm (Bamline_T this);
120 114 
 extern char
121 115 
 Bamline_splice_strand (Bamline_T this);
122 116
... ... 
@@ -149,12 +143,6 @@ Bamread_next_bamline_set (int *nlines, Bamline_T *prev_bamline,
149 143 
 			  bool need_unique_p, bool need_primary_p, bool ignore_duplicates_p,
150 144 
 			  bool need_concordant_p);
151 145
152 
-extern Bamline_T **
153 
-Bamread_block (int **nlines, Genomicpos_T chrstart, Genomicpos_T chrend,
154 
-	       T this, char *desired_read_group, int minimum_mapq, int good_unique_mapq, int maximum_nhits,
155 
-	       bool need_unique_p, bool need_primary_p, bool ignore_duplicates_p,
156 
-	       bool need_concordant_p);
157 
-
158 146 
 extern Bamline_T
159 147 
 Bamread_get_acc (T this, char *desired_chr, Genomicpos_T desired_chrpos, char *desired_acc);
160 148
... ... 
@@ -181,8 +169,6 @@ Bamstore_table_free (Uinttable_T *bamstore_table);
181 169
182 170 
 typedef struct Bampair_T *Bampair_T;
183 171
184 
-extern char *
185 
-Bampair_acc (Bampair_T this);
186 172 
 extern Bamline_T
187 173 
 Bampair_bamline_low (Bampair_T this);
188 174 
 extern Bamline_T
Browse code

update gstruct/bamtally

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@101176 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 25/03/2015 20:25:05
Showing 1 changed files
src/gstruct/src/bamread.h
History View file @ f58d4e9
... ... 
@@ -1,4 +1,4 @@
1 
-/* $Id: bamread.h 141010 2014-07-09 16:34:11Z twu $ */
1 
+/* $Id: bamread.h 160725 2015-03-11 16:45:17Z twu $ */
2 2 
 #ifndef BAMREAD_INCLUDED
3 3 
 #define BAMREAD_INCLUDED
4 4 
 /* Cannot use bool, since it appears to conflict with samtools */
... ... 
@@ -43,8 +43,8 @@ extern int
43 43 
 Bamread_next_line (T this, char **acc, unsigned int *flag, int *mapq, char **chr, Genomicpos_T *chrpos,
44 44 
 		   char **mate_chr, Genomicpos_T *mate_chrpos,
45 45 
 		   Intlist_T *cigartypes, Uintlist_T *cigarlengths, int *cigarlength,
46 
-		   int *readlength, char **read, char **quality_string, char **read_group,
47 
-		   bool *terminalp);
46 
+		   int *readlength, char **read, char **quality_string, char **hardclip, char **hardclip_quality,
47 
+		   char **read_group, bool *terminalp);
48 48
49 49 
 typedef struct Bamline_T *Bamline_T;
50 50
... ... 
@@ -85,7 +85,7 @@ Bamline_cigar_types (Bamline_T this);
85 85 
 extern Uintlist_T
86 86 
 Bamline_cigar_npositions (Bamline_T this);
87 87 
 extern Intlist_T
88 
-Bamline_diffcigar (Uintlist_T *npositions, Uintlist_T *chrpositions, Bamline_T this);
88 
+Bamline_diffcigar (int *min_overhang, Uintlist_T *npositions, Uintlist_T *chrpositions, Bamline_T this);
89 89 
 extern int
90 90 
 Bamline_cigar_querylength (Bamline_T this);
91 91 
 extern void
... ... 
@@ -98,6 +98,10 @@ extern char *
98 98 
 Bamline_read (Bamline_T this);
99 99 
 extern char *
100 100 
 Bamline_quality_string (Bamline_T this);
101 
+extern char *
102 
+Bamline_hardclip (Bamline_T this);
103 
+extern char *
104 
+Bamline_hardclip_quality (Bamline_T this);
101 105 
 extern bool
102 106 
 Bamline_terminalp (Bamline_T this);
103 107 
 extern char *
... ... 
@@ -111,6 +115,8 @@ extern void
111 115 
 Bamline_print_new_mate (FILE *fp, Bamline_T this, char *mate_chr, Genomicpos_T mate_chrpos_low,
112 116 
 			int insert_length);
113 117
118 
+extern int
119 
+Bamline_nm (Bamline_T this);
114 120 
 extern char
115 121 
 Bamline_splice_strand (Bamline_T this);
116 122
... ... 
@@ -143,6 +149,12 @@ Bamread_next_bamline_set (int *nlines, Bamline_T *prev_bamline,
143 149 
 			  bool need_unique_p, bool need_primary_p, bool ignore_duplicates_p,
144 150 
 			  bool need_concordant_p);
145 151
152 
+extern Bamline_T **
153 
+Bamread_block (int **nlines, Genomicpos_T chrstart, Genomicpos_T chrend,
154 
+	       T this, char *desired_read_group, int minimum_mapq, int good_unique_mapq, int maximum_nhits,
155 
+	       bool need_unique_p, bool need_primary_p, bool ignore_duplicates_p,
156 
+	       bool need_concordant_p);
157 
+
146 158 
 extern Bamline_T
147 159 
 Bamread_get_acc (T this, char *desired_chr, Genomicpos_T desired_chrpos, char *desired_acc);
148 160
... ... 
@@ -169,6 +181,8 @@ Bamstore_table_free (Uinttable_T *bamstore_table);
169 181
170 182 
 typedef struct Bampair_T *Bampair_T;
171 183
184 
+extern char *
185 
+Bampair_acc (Bampair_T this);
172 186 
 extern Bamline_T
173 187 
 Bampair_bamline_low (Bampair_T this);
174 188 
 extern Bamline_T
Browse code

add codon tally support. No vbump yet

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@93316 bc3139a8-67e5-0310-9ffc-ced21a209358

Gabriel Becker authored on 11/08/2014 23:42:48
Showing 1 changed files
src/gstruct/src/bamread.h
History View file @ c78be69
... ... 
@@ -1,4 +1,4 @@
1 
-/* $Id: bamread.h 137605 2014-05-30 00:33:41Z twu $ */
1 
+/* $Id: bamread.h 141010 2014-07-09 16:34:11Z twu $ */
2 2 
 #ifndef BAMREAD_INCLUDED
3 3 
 #define BAMREAD_INCLUDED
4 4 
 /* Cannot use bool, since it appears to conflict with samtools */
... ... 
@@ -64,6 +64,8 @@ extern int
64 64 
 Bamline_nhits (Bamline_T this);
65 65 
 extern bool
66 66 
 Bamline_good_unique_p (Bamline_T this);
67 
+extern bool
68 
+Bamline_perfect_match_p (Bamline_T this);
67 69 
 extern int
68 70 
 Bamline_mapq (Bamline_T this);
69 71 
 extern char *
... ... 
@@ -104,7 +106,7 @@ extern void
104 106 
 Bamline_print (FILE *fp, Bamline_T this, unsigned int newflag, int quality_score_adj);
105 107 
 extern void
106 108 
 Bamline_print_new_cigar (FILE *fp, Bamline_T this, Genomicpos_T chrpos_low, char *new_cigar,
107 
-			 char *new_md_string);
109 
+			 char *new_md_string, int quality_score_adj);
108 110 
 extern void
109 111 
 Bamline_print_new_mate (FILE *fp, Bamline_T this, char *mate_chr, Genomicpos_T mate_chrpos_low,
110 112 
 			int insert_length);
... ... 
@@ -116,6 +118,12 @@ extern char
116 118 
 Bamline_strand (Bamline_T this, Genome_T genome, IIT_T chromosome_iit);
117 119 
 extern Genomicpos_T
118 120 
 Bamline_chrpos_high (Bamline_T this);
121 
+extern Genomicpos_T
122 
+Bamline_chrpos_high_noclip (Bamline_T this);
123 
+extern Genomicpos_T
124 
+Bamline_total_ins (Bamline_T this);
125 
+extern int
126 
+Bamline_nmismatches (Bamline_T this);
119 127
120 128
121 129 
 extern void
... ... 
@@ -125,6 +133,17 @@ Bamread_next_bamline (T this, char *desired_read_group, int minimum_mapq, int go
125 133 
 		      bool need_unique_p, bool need_primary_p, bool ignore_duplicates_p,
126 134 
 		      bool need_concordant_p);
127 135 
 extern Bamline_T
136 
+Bamread_next_indel_bamline (T this, char *desired_read_group, int minimum_mapq, int good_unique_mapq, int maximum_nhits,
137 
+			    bool need_unique_p, bool need_primary_p, bool ignore_duplicates_p,
138 
+			    bool need_concordant_p);
139 
+
140 
+extern Bamline_T *
141 
+Bamread_next_bamline_set (int *nlines, Bamline_T *prev_bamline,
142 
+			  T this, char *desired_read_group, int minimum_mapq, int good_unique_mapq, int maximum_nhits,
143 
+			  bool need_unique_p, bool need_primary_p, bool ignore_duplicates_p,
144 
+			  bool need_concordant_p);
145 
+
146 
+extern Bamline_T
128 147 
 Bamread_get_acc (T this, char *desired_chr, Genomicpos_T desired_chrpos, char *desired_acc);
129 148
130 149
Browse code

update gstruct (hopefully fix build)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@91068 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 06/06/2014 22:10:15
Showing 1 changed files
src/gstruct/src/bamread.h
History View file @ 52b3ca6
... ... 
@@ -1,4 +1,4 @@
1 
-/* $Id: bamread.h 134418 2014-04-25 22:14:34Z twu $ */
1 
+/* $Id: bamread.h 137605 2014-05-30 00:33:41Z twu $ */
2 2 
 #ifndef BAMREAD_INCLUDED
3 3 
 #define BAMREAD_INCLUDED
4 4 
 /* Cannot use bool, since it appears to conflict with samtools */
... ... 
@@ -82,6 +82,8 @@ extern Intlist_T
82 82 
 Bamline_cigar_types (Bamline_T this);
83 83 
 extern Uintlist_T
84 84 
 Bamline_cigar_npositions (Bamline_T this);
85 
+extern Intlist_T
86 
+Bamline_diffcigar (Uintlist_T *npositions, Uintlist_T *chrpositions, Bamline_T this);
85 87 
 extern int
86 88 
 Bamline_cigar_querylength (Bamline_T this);
87 89 
 extern void
... ... 
@@ -103,6 +105,9 @@ Bamline_print (FILE *fp, Bamline_T this, unsigned int newflag, int quality_score
103 105 
 extern void
104 106 
 Bamline_print_new_cigar (FILE *fp, Bamline_T this, Genomicpos_T chrpos_low, char *new_cigar,
105 107 
 			 char *new_md_string);
108 
+extern void
109 
+Bamline_print_new_mate (FILE *fp, Bamline_T this, char *mate_chr, Genomicpos_T mate_chrpos_low,
110 
+			int insert_length);
106 111
107 112 
 extern char
108 113 
 Bamline_splice_strand (Bamline_T this);
Browse code

update bam_tally, mostly to fix memory leaks but we are also moving towards a decent indel realigner

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@89723 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 30/04/2014 17:04:17
Showing 1 changed files
src/gstruct/src/bamread.h
History View file @ 144f6bb
... ... 
@@ -1,4 +1,4 @@
1 
-/* $Id: bamread.h 129099 2014-03-04 18:44:44Z twu $ */
1 
+/* $Id: bamread.h 134418 2014-04-25 22:14:34Z twu $ */
2 2 
 #ifndef BAMREAD_INCLUDED
3 3 
 #define BAMREAD_INCLUDED
4 4 
 /* Cannot use bool, since it appears to conflict with samtools */
... ... 
@@ -70,6 +70,8 @@ extern char *
70 70 
 Bamline_chr (Bamline_T this);
71 71 
 extern Genomicpos_T
72 72 
 Bamline_chrpos_low (Bamline_T this);
73 
+extern Genomicpos_T
74 
+Bamline_chrpos_low_noclip (Bamline_T this);
73 75 
 extern char *
74 76 
 Bamline_mate_chr (Bamline_T this);
75 77 
 extern Genomicpos_T
... ... 
@@ -98,6 +100,9 @@ extern char *
98 100 
 Bamline_read_group (Bamline_T this);
99 101 
 extern void
100 102 
 Bamline_print (FILE *fp, Bamline_T this, unsigned int newflag, int quality_score_adj);
103 
+extern void
104 
+Bamline_print_new_cigar (FILE *fp, Bamline_T this, Genomicpos_T chrpos_low, char *new_cigar,
105 
+			 char *new_md_string);
101 106
102 107 
 extern char
103 108 
 Bamline_splice_strand (Bamline_T this);
Browse code

update GSTRUCT (bam_tally); add include_soft_clip parameter for counting over soft clips of a given max length (more accurate allele frequency)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@88343 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 02/04/2014 22:03:40
Showing 1 changed files
src/gstruct/src/bamread.h
History View file @ 17db5e7
... ... 
@@ -1,4 +1,4 @@
1 
-/* $Id: bamread.h 108654 2013-09-19 23:11:00Z twu $ */
1 
+/* $Id: bamread.h 129099 2014-03-04 18:44:44Z twu $ */
2 2 
 #ifndef BAMREAD_INCLUDED
3 3 
 #define BAMREAD_INCLUDED
4 4 
 /* Cannot use bool, since it appears to conflict with samtools */
... ... 
@@ -43,7 +43,8 @@ extern int
43 43 
 Bamread_next_line (T this, char **acc, unsigned int *flag, int *mapq, char **chr, Genomicpos_T *chrpos,
44 44 
 		   char **mate_chr, Genomicpos_T *mate_chrpos,
45 45 
 		   Intlist_T *cigartypes, Uintlist_T *cigarlengths, int *cigarlength,
46 
-		   int *readlength, char **read, char **quality_string, char **read_group);
46 
+		   int *readlength, char **read, char **quality_string, char **read_group,
47 
+		   bool *terminalp);
47 48
48 49 
 typedef struct Bamline_T *Bamline_T;
49 50
... ... 
@@ -91,6 +92,8 @@ extern char *
91 92 
 Bamline_read (Bamline_T this);
92 93 
 extern char *
93 94 
 Bamline_quality_string (Bamline_T this);
95 
+extern bool
96 
+Bamline_terminalp (Bamline_T this);
94 97 
 extern char *
95 98 
 Bamline_read_group (Bamline_T this);
96 99 
 extern void
Browse code

update to latest gstruct; brings faster bam_tally (for high coverage regions) and read-group filtering support in bam_tally

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@80611 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 20/09/2013 02:05:42
Showing 1 changed files
src/gstruct/src/bamread.h
History View file @ 4d5cc80
... ... 
@@ -1,4 +1,4 @@
1 
-/* $Id: bamread.h 87713 2013-03-01 18:32:34Z twu $ */
1 
+/* $Id: bamread.h 108654 2013-09-19 23:11:00Z twu $ */
2 2 
 #ifndef BAMREAD_INCLUDED
3 3 
 #define BAMREAD_INCLUDED
4 4 
 /* Cannot use bool, since it appears to conflict with samtools */
... ... 
@@ -43,7 +43,7 @@ extern int
43 43 
 Bamread_next_line (T this, char **acc, unsigned int *flag, int *mapq, char **chr, Genomicpos_T *chrpos,
44 44 
 		   char **mate_chr, Genomicpos_T *mate_chrpos,
45 45 
 		   Intlist_T *cigartypes, Uintlist_T *cigarlengths, int *cigarlength,
46 
-		   int *readlength, char **read, char **quality_string);
46 
+		   int *readlength, char **read, char **quality_string, char **read_group);
47 47
48 48 
 typedef struct Bamline_T *Bamline_T;
49 49
... ... 
@@ -83,12 +83,16 @@ extern int
83 83 
 Bamline_cigar_querylength (Bamline_T this);
84 84 
 extern void
85 85 
 Bamread_print_cigar (FILE *fp, Bamline_T this);
86 
+extern char *
87 
+Bamline_cigar_string (Bamline_T this);
86 88 
 extern int
87 89 
 Bamline_readlength (Bamline_T this);
88 90 
 extern char *
89 91 
 Bamline_read (Bamline_T this);
90 92 
 extern char *
91 93 
 Bamline_quality_string (Bamline_T this);
94 
+extern char *
95 
+Bamline_read_group (Bamline_T this);
92 96 
 extern void
93 97 
 Bamline_print (FILE *fp, Bamline_T this, unsigned int newflag, int quality_score_adj);
94 98
... ... 
@@ -104,7 +108,7 @@ Bamline_chrpos_high (Bamline_T this);
104 108 
 extern void
105 109 
 Bamline_free (Bamline_T *old);
106 110 
 extern Bamline_T
107 
-Bamread_next_bamline (T this, int minimum_mapq, int good_unique_mapq, int maximum_nhits,
111 
+Bamread_next_bamline (T this, char *desired_read_group, int minimum_mapq, int good_unique_mapq, int maximum_nhits,
108 112 
 		      bool need_unique_p, bool need_primary_p, bool ignore_duplicates_p,
109 113 
 		      bool need_concordant_p);
110 114 
 extern Bamline_T
... ... 
@@ -160,14 +164,14 @@ Bampair_details (Uintlist_T *chrpos_lows, Uintlist_T *chrpos_highs,
160 164 
 		 Bampair_T this);
161 165
162 166 
 extern List_T
163 
-Bamread_all_pairs (T bamreader, int minimum_mapq, int good_unique_mapq, int maximum_nhits,
167 
+Bamread_all_pairs (T bamreader, char *desired_read_group, int minimum_mapq, int good_unique_mapq, int maximum_nhits,
164 168 
 		   bool need_unique_p, bool need_primary_p, bool ignore_duplicates_p,
165 169 
 		   bool need_concordant_p);
166 170
167 171 
 extern int
168 172 
 Bampair_compute_levels (List_T bampairs, Genomicpos_T mincoord,
169 173 
 			Genomicpos_T maxcoord, int max_allowed_levels,
170 
-			double xfactor, Genomicpos_T min_pairlength);
174 
+			double xfactor, Genomicpos_T min_pairlength, bool only_internal_p);
171 175
172 176
173 177 
 #undef T
Browse code

Update gstruct; bam_tally now supports ignoring PCR/optical duplicates.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@74870 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 26/03/2013 21:37:34
Showing 1 changed files
src/gstruct/src/bamread.h
History View file @ 95e6ece
... ... 
@@ -1,4 +1,4 @@
1 
-/* $Id: bamread.h 75138 2012-09-27 18:00:15Z twu $ */
1 
+/* $Id: bamread.h 87713 2013-03-01 18:32:34Z twu $ */
2 2 
 #ifndef BAMREAD_INCLUDED
3 3 
 #define BAMREAD_INCLUDED
4 4 
 /* Cannot use bool, since it appears to conflict with samtools */
... ... 
@@ -45,7 +45,6 @@ Bamread_next_line (T this, char **acc, unsigned int *flag, int *mapq, char **chr
45 45 
 		   Intlist_T *cigartypes, Uintlist_T *cigarlengths, int *cigarlength,
46 46 
 		   int *readlength, char **read, char **quality_string);
47 47
48 
-
49 48 
 typedef struct Bamline_T *Bamline_T;
50 49
51 50 
 extern char *
... ... 
@@ -83,7 +82,7 @@ Bamline_cigar_npositions (Bamline_T this);
83 82 
 extern int
84 83 
 Bamline_cigar_querylength (Bamline_T this);
85 84 
 extern void
86 
-Bamread_print_cigar (Bamline_T this);
85 
+Bamread_print_cigar (FILE *fp, Bamline_T this);
87 86 
 extern int
88 87 
 Bamline_readlength (Bamline_T this);
89 88 
 extern char *
... ... 
@@ -91,7 +90,7 @@ Bamline_read (Bamline_T this);
91 90 
 extern char *
92 91 
 Bamline_quality_string (Bamline_T this);
93 92 
 extern void
94 
-Bamline_print (FILE *fp, Bamline_T this, unsigned int newflag);
93 
+Bamline_print (FILE *fp, Bamline_T this, unsigned int newflag, int quality_score_adj);
95 94
96 95 
 extern char
97 96 
 Bamline_splice_strand (Bamline_T this);
... ... 
@@ -106,7 +105,10 @@ extern void
106 105 
 Bamline_free (Bamline_T *old);
107 106 
 extern Bamline_T
108 107 
 Bamread_next_bamline (T this, int minimum_mapq, int good_unique_mapq, int maximum_nhits,
109 
-		      bool need_unique_p, bool need_primary_p, bool need_concordant_p);
108 
+		      bool need_unique_p, bool need_primary_p, bool ignore_duplicates_p,
109 
+		      bool need_concordant_p);
110 
+extern Bamline_T
111 
+Bamread_get_acc (T this, char *desired_chr, Genomicpos_T desired_chrpos, char *desired_acc);
110 112
111 113
112 114 
 typedef struct Bamstore_T *Bamstore_T;
... ... 
@@ -131,6 +133,10 @@ Bamstore_table_free (Uinttable_T *bamstore_table);
131 133
132 134 
 typedef struct Bampair_T *Bampair_T;
133 135
136 
+extern Bamline_T
137 
+Bampair_bamline_low (Bampair_T this);
138 
+extern Bamline_T
139 
+Bampair_bamline_high (Bampair_T this);
134 140 
 extern Genomicpos_T
135 141 
 Bampair_chrpos_low (Bampair_T this);
136 142 
 extern Genomicpos_T
... ... 
@@ -147,7 +153,7 @@ Bampair_primaryp (Bampair_T this);
147 153 
 extern void
148 154 
 Bampair_free (Bampair_T *old);
149 155 
 extern void
150 
-Bampair_print (FILE *fp, Bampair_T this);
156 
+Bampair_print (FILE *fp, Bampair_T this, int quality_score_adj);
151 157 
 extern void
152 158 
 Bampair_details (Uintlist_T *chrpos_lows, Uintlist_T *chrpos_highs,
153 159 
 		 Uintlist_T *splice_lows, Uintlist_T *splice_highs, Intlist_T *splice_signs,
... ... 
@@ -155,7 +161,8 @@ Bampair_details (Uintlist_T *chrpos_lows, Uintlist_T *chrpos_highs,
155 161
156 162 
 extern List_T
157 163 
 Bamread_all_pairs (T bamreader, int minimum_mapq, int good_unique_mapq, int maximum_nhits,
158 
-		   bool need_unique_p, bool need_primary_p, bool need_concordant_p);
164 
+		   bool need_unique_p, bool need_primary_p, bool ignore_duplicates_p,
165 
+		   bool need_concordant_p);
159 166
160 167 
 extern int
161 168 
 Bampair_compute_levels (List_T bampairs, Genomicpos_T mincoord,
Browse code

added new version of gmap and gstruct src code

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@70363 bc3139a8-67e5-0310-9ffc-ced21a209358

Cory Barr authored on 10/10/2012 00:38:59
Showing 1 changed files
src/gstruct/src/bamread.h
History View file @ 36cb64f
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,168 @@
1 
+/* $Id: bamread.h 75138 2012-09-27 18:00:15Z twu $ */
2 
+#ifndef BAMREAD_INCLUDED
3 
+#define BAMREAD_INCLUDED
4 
+/* Cannot use bool, since it appears to conflict with samtools */
5 
+#include <stdio.h>
6 
+#include "genomicpos.h"
7 
+#include "intlist.h"
8 
+#include "uintlist.h"
9 
+#include "genome.h"
10 
+#include "iit-read.h"
11 
+
12 
+#include "table.h"
13 
+#include "uinttable.h"
14 
+#include "chrom.h"
15 
+#include "list.h"
16 
+
17 
+
18 
+#define T Bamreader_T
19 
+typedef struct T *T;
20 
+
21 
+extern void
22 
+Bamread_free (T *old);
23 
+
24 
+extern T
25 
+Bamread_new (char *filename);
26 
+
27 
+extern void
28 
+Bamread_write_header (T this);
29 
+
30 
+extern Genomicpos_T
31 
+Bamread_chrlength (T this, char *chr);
32 
+
33 
+extern bool
34 
+Bamread_limit_region (T this, char *chr, Genomicpos_T chrstart, Genomicpos_T chrend);
35 
+
36 
+extern void
37 
+Bamread_unlimit_region (T this);
38 
+
39 
+extern int
40 
+Bamread_nreads (int *npositions, T this, char *chr, Genomicpos_T chrpos1, Genomicpos_T chrpos2);
41 
+
42 
+extern int
43 
+Bamread_next_line (T this, char **acc, unsigned int *flag, int *mapq, char **chr, Genomicpos_T *chrpos,
44 
+		   char **mate_chr, Genomicpos_T *mate_chrpos,
45 
+		   Intlist_T *cigartypes, Uintlist_T *cigarlengths, int *cigarlength,
46 
+		   int *readlength, char **read, char **quality_string);
47 
+
48 
+
49 
+typedef struct Bamline_T *Bamline_T;
50 
+
51 
+extern char *
52 
+Bamline_acc (Bamline_T this);
53 
+extern unsigned int
54 
+Bamline_flag (Bamline_T this);
55 
+extern int
56 
+Bamline_concordantp (Bamline_T this);
57 
+extern int
58 
+Bamline_lowend_p (Bamline_T this);
59 
+extern int
60 
+Bamline_paired_read_p (Bamline_T this);
61 
+extern int
62 
+Bamline_firstend_p (Bamline_T this);
63 
+extern int
64 
+Bamline_nhits (Bamline_T this);
65 
+extern bool
66 
+Bamline_good_unique_p (Bamline_T this);
67 
+extern int
68 
+Bamline_mapq (Bamline_T this);
69 
+extern char *
70 
+Bamline_chr (Bamline_T this);
71 
+extern Genomicpos_T
72 
+Bamline_chrpos_low (Bamline_T this);
73 
+extern char *
74 
+Bamline_mate_chr (Bamline_T this);
75 
+extern Genomicpos_T
76 
+Bamline_mate_chrpos_low (Bamline_T this);
77 
+extern int
78 
+Bamline_insert_length (Bamline_T this);
79 
+extern Intlist_T
80 
+Bamline_cigar_types (Bamline_T this);
81 
+extern Uintlist_T
82 
+Bamline_cigar_npositions (Bamline_T this);
83 
+extern int
84 
+Bamline_cigar_querylength (Bamline_T this);
85 
+extern void
86 
+Bamread_print_cigar (Bamline_T this);
87 
+extern int
88 
+Bamline_readlength (Bamline_T this);
89 
+extern char *
90 
+Bamline_read (Bamline_T this);
91 
+extern char *
92 
+Bamline_quality_string (Bamline_T this);
93 
+extern void
94 
+Bamline_print (FILE *fp, Bamline_T this, unsigned int newflag);
95 
+
96 
+extern char
97 
+Bamline_splice_strand (Bamline_T this);
98 
+
99 
+extern char
100 
+Bamline_strand (Bamline_T this, Genome_T genome, IIT_T chromosome_iit);
101 
+extern Genomicpos_T
102 
+Bamline_chrpos_high (Bamline_T this);
103 
+
104 
+
105 
+extern void
106 
+Bamline_free (Bamline_T *old);
107 
+extern Bamline_T
108 
+Bamread_next_bamline (T this, int minimum_mapq, int good_unique_mapq, int maximum_nhits,
109 
+		      bool need_unique_p, bool need_primary_p, bool need_concordant_p);
110 
+
111 
+
112 
+typedef struct Bamstore_T *Bamstore_T;
113 
+
114 
+extern void
115 
+Bamstore_free (Bamstore_T *old);
116 
+
117 
+extern Bamstore_T
118 
+Bamstore_new (Genomicpos_T chrpos);
119 
+
120 
+extern Bamline_T
121 
+Bamstore_get (Table_T bamstore_chrtable, char *chr, Genomicpos_T low, char *acc,
122 
+	      Genomicpos_T mate_low);
123 
+
124 
+extern void
125 
+Bamstore_add_at_low (Table_T bamstore_chrtable, char *chr, Genomicpos_T low,
126 
+		     Bamline_T bamline);
127 
+
128 
+extern void
129 
+Bamstore_table_free (Uinttable_T *bamstore_table);
130 
+
131 
+
132 
+typedef struct Bampair_T *Bampair_T;
133 
+
134 
+extern Genomicpos_T
135 
+Bampair_chrpos_low (Bampair_T this);
136 
+extern Genomicpos_T
137 
+Bampair_chrpos_high (Bampair_T this);
138 
+extern int
139 
+Bampair_level (Bampair_T this);
140 
+extern bool
141 
+Bampair_good_unique_p (Bampair_T this);
142 
+extern bool
143 
+Bampair_uniquep (Bampair_T this);
144 
+extern bool
145 
+Bampair_primaryp (Bampair_T this);
146 
+
147 
+extern void
148 
+Bampair_free (Bampair_T *old);
149 
+extern void
150 
+Bampair_print (FILE *fp, Bampair_T this);
151 
+extern void
152 
+Bampair_details (Uintlist_T *chrpos_lows, Uintlist_T *chrpos_highs,
153 
+		 Uintlist_T *splice_lows, Uintlist_T *splice_highs, Intlist_T *splice_signs,
154 
+		 Bampair_T this);
155 
+
156 
+extern List_T
157 
+Bamread_all_pairs (T bamreader, int minimum_mapq, int good_unique_mapq, int maximum_nhits,
158 
+		   bool need_unique_p, bool need_primary_p, bool need_concordant_p);
159 
+
160 
+extern int
161 
+Bampair_compute_levels (List_T bampairs, Genomicpos_T mincoord,
162 
+			Genomicpos_T maxcoord, int max_allowed_levels,
163 
+			double xfactor, Genomicpos_T min_pairlength);
164 
+
165 
+
166 
+#undef T
167 
+#endif
168 
+
Browse code

removing old gstruct and gmap src code before adding new src

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@70362 bc3139a8-67e5-0310-9ffc-ced21a209358

Cory Barr authored on 10/10/2012 00:34:30
Showing 1 changed files
src/gstruct/src/bamread.h
History View file @ 5fa057e
1 1 
deleted file mode 100644
... ... 
@@ -1,165 +0,0 @@
1 
-/* $Id: bamread.h 55603 2012-01-10 01:40:54Z twu $ */
2 
-#ifndef BAMREAD_INCLUDED
3 
-#define BAMREAD_INCLUDED
4 
-/* Cannot use bool, since it appears to conflict with samtools */
5 
-#include <stdio.h>
6 
-#include "genomicpos.h"
7 
-#include "intlist.h"
8 
-#include "uintlist.h"
9 
-#include "genome.h"
10 
-#include "iit-read.h"
11 
-
12 
-#include "table.h"
13 
-#include "uinttable.h"
14 
-#include "chrom.h"
15 
-#include "list.h"
16 
-
17 
-
18 
-#define T Bamreader_T
19 
-typedef struct T *T;
20 
-
21 
-extern void
22 
-Bamread_free (T *old);
23 
-
24 
-extern T
25 
-Bamread_new (char *filename);
26 
-
27 
-extern void
28 
-Bamread_write_header (T this);
29 
-
30 
-extern Genomicpos_T
31 
-Bamread_chrlength (T this, char *chr);
32 
-
33 
-extern bool
34 
-Bamread_limit_region (T this, char *chr, Genomicpos_T chrstart, Genomicpos_T chrend);
35 
-
36 
-extern void
37 
-Bamread_unlimit_region (T this);
38 
-
39 
-extern int
40 
-Bamread_nreads (int *npositions, T this, char *chr, Genomicpos_T chrpos1, Genomicpos_T chrpos2);
41 
-
42 
-extern int
43 
-Bamread_next_line (T this, char **acc, unsigned int *flag, int *mapq, char **chr, Genomicpos_T *chrpos,
44 
-		   char **mate_chr, Genomicpos_T *mate_chrpos,
45 
-		   Intlist_T *cigartypes, Uintlist_T *cigarlengths, int *cigarlength,
46 
-		   int *readlength, char **read, char **quality_string);
47 
-
48 
-
49 
-typedef struct Bamline_T *Bamline_T;
50 
-
51 
-extern char *
52 
-Bamline_acc (Bamline_T this);
53 
-extern unsigned int
54 
-Bamline_flag (Bamline_T this);
55 
-extern int
56 
-Bamline_concordantp (Bamline_T this);
57 
-extern int
58 
-Bamline_lowend_p (Bamline_T this);
59 
-extern int
60 
-Bamline_firstend_p (Bamline_T this);
61 
-extern int
62 
-Bamline_nhits (Bamline_T this);
63 
-extern bool
64 
-Bamline_good_unique_p (Bamline_T this);
65 
-extern int
66 
-Bamline_mapq (Bamline_T this);
67 
-extern char *
68 
-Bamline_chr (Bamline_T this);
69 
-extern Genomicpos_T
70 
-Bamline_chrpos_low (Bamline_T this);
71 
-extern char *
72 
-Bamline_mate_chr (Bamline_T this);
73 
-extern Genomicpos_T
74 
-Bamline_mate_chrpos_low (Bamline_T this);
75 
-extern int
76 
-Bamline_insert_length (Bamline_T this);
77 
-extern Intlist_T
78 
-Bamline_cigar_types (Bamline_T this);
79 
-extern Uintlist_T
80 
-Bamline_cigar_npositions (Bamline_T this);
81 
-extern int
82 
-Bamline_cigar_querylength (Bamline_T this);
83 
-extern void
84 
-Bamread_print_cigar (Bamline_T this);
85 
-extern int
86 
-Bamline_readlength (Bamline_T this);
87 
-extern char *
88 
-Bamline_read (Bamline_T this);
89 
-extern char *
90 
-Bamline_quality_string (Bamline_T this);
91 
-extern void
92 
-Bamline_print (FILE *fp, Bamline_T this, unsigned int newflag);
93 
-
94 
-extern char
95 
-Bamline_splice_strand (Bamline_T this);
96 
-extern char
97 
-Bamline_strand (Bamline_T this, Genome_T genome, IIT_T chromosome_iit);
98 
-extern Genomicpos_T
99 
-Bamline_chrpos_high (Bamline_T this);
100 
-
101 
-
102 
-extern void
103 
-Bamline_free (Bamline_T *old);
104 
-extern Bamline_T
105 
-Bamread_next_bamline (T this, int minimum_mapq, int good_unique_mapq, int maximum_nhits,
106 
-		      bool need_unique_p, bool need_primary_p, bool need_concordant_p);
107 
-
108 
-
109 
-typedef struct Bamstore_T *Bamstore_T;
110 
-
111 
-extern void
112 
-Bamstore_free (Bamstore_T *old);
113 
-
114 
-extern Bamstore_T
115 
-Bamstore_new (Genomicpos_T chrpos);
116 
-
117 
-extern Bamline_T
118 
-Bamstore_get (Table_T bamstore_chrtable, char *chr, Genomicpos_T low, char *acc,
119 
-	      Genomicpos_T mate_low);
120 
-
121 
-extern void
122 
-Bamstore_add_at_low (Table_T bamstore_chrtable, char *chr, Genomicpos_T low,
123 
-		     Bamline_T bamline);
124 
-
125 
-extern void
126 
-Bamstore_table_free (Uinttable_T *bamstore_table);
127 
-
128 
-
129 
-typedef struct Bampair_T *Bampair_T;
130 
-
131 
-extern Genomicpos_T
132 
-Bampair_chrpos_low (Bampair_T this);
133 
-extern Genomicpos_T
134 
-Bampair_chrpos_high (Bampair_T this);
135 
-extern int
136 
-Bampair_level (Bampair_T this);
137 
-extern bool
138 
-Bampair_good_unique_p (Bampair_T this);
139 
-extern bool
140 
-Bampair_uniquep (Bampair_T this);
141 
-extern bool
142 
-Bampair_primaryp (Bampair_T this);
143 
-
144 
-extern void
145 
-Bampair_free (Bampair_T *old);
146 
-extern void
147