22#include <ctype.h>
33#include <string.h>
44#include <stdio.h>
5+ #include "utils.h"
56#include "bamlite.h"
67
78/*********************
@@ -53,7 +54,7 @@ int bam_is_be;
5354bam_header_t * bam_header_init ()
5455{
5556 bam_is_be = bam_is_big_endian ();
56- return (bam_header_t * )calloc (1 , sizeof (bam_header_t ));
57+ return (bam_header_t * )xcalloc (1 , sizeof (bam_header_t ));
5758}
5859
5960void bam_header_destroy (bam_header_t * header )
@@ -62,11 +63,11 @@ void bam_header_destroy(bam_header_t *header)
6263 if (header == 0 ) return ;
6364 if (header -> target_name ) {
6465 for (i = 0 ; i < header -> n_targets ; ++ i )
65- free (header -> target_name [i ]);
66+ if (header -> target_name [i ]) free (header -> target_name [i ]);
67+ if (header -> target_len ) free (header -> target_len );
6668 free (header -> target_name );
67- free (header -> target_len );
6869 }
69- free (header -> text );
70+ if ( header -> text ) free (header -> text );
7071 free (header );
7172}
7273
@@ -80,28 +81,33 @@ bam_header_t *bam_header_read(bamFile fp)
8081 magic_len = bam_read (fp , buf , 4 );
8182 if (magic_len != 4 || strncmp (buf , "BAM\001" , 4 ) != 0 ) {
8283 fprintf (stderr , "[bam_header_read] invalid BAM binary header (this is not a BAM file).\n" );
83- return 0 ;
84+ return NULL ;
8485 }
8586 header = bam_header_init ();
8687 // read plain text and the number of reference sequences
87- bam_read (fp , & header -> l_text , 4 );
88+ if ( bam_read (fp , & header -> l_text , 4 ) != 4 ) goto fail ;
8889 if (bam_is_be ) bam_swap_endian_4p (& header -> l_text );
89- header -> text = (char * )calloc (header -> l_text + 1 , 1 );
90- bam_read (fp , header -> text , header -> l_text );
91- bam_read (fp , & header -> n_targets , 4 );
90+ header -> text = (char * )xcalloc (header -> l_text + 1 , 1 );
91+ if ( bam_read (fp , header -> text , header -> l_text ) != header -> l_text ) goto fail ;
92+ if ( bam_read (fp , & header -> n_targets , 4 ) != 4 ) goto fail ;
9293 if (bam_is_be ) bam_swap_endian_4p (& header -> n_targets );
9394 // read reference sequence names and lengths
94- header -> target_name = (char * * )calloc (header -> n_targets , sizeof (char * ));
95- header -> target_len = (uint32_t * )calloc (header -> n_targets , 4 );
95+ header -> target_name = (char * * )xcalloc (header -> n_targets , sizeof (char * ));
96+ header -> target_len = (uint32_t * )xcalloc (header -> n_targets , 4 );
9697 for (i = 0 ; i != header -> n_targets ; ++ i ) {
97- bam_read (fp , & name_len , 4 );
98+ if ( bam_read (fp , & name_len , 4 ) != 4 ) goto fail ;
9899 if (bam_is_be ) bam_swap_endian_4p (& name_len );
99- header -> target_name [i ] = (char * )calloc (name_len , 1 );
100- bam_read (fp , header -> target_name [i ], name_len );
101- bam_read (fp , & header -> target_len [i ], 4 );
100+ header -> target_name [i ] = (char * )xcalloc (name_len , 1 );
101+ if (bam_read (fp , header -> target_name [i ], name_len ) != name_len ) {
102+ goto fail ;
103+ }
104+ if (bam_read (fp , & header -> target_len [i ], 4 ) != 4 ) goto fail ;
102105 if (bam_is_be ) bam_swap_endian_4p (& header -> target_len [i ]);
103106 }
104107 return header ;
108+ fail :
109+ bam_header_destroy (header );
110+ return NULL ;
105111}
106112
107113static void swap_endian_data (const bam1_core_t * c , int data_len , uint8_t * data )
@@ -146,7 +152,7 @@ int bam_read1(bamFile fp, bam1_t *b)
146152 if (b -> m_data < b -> data_len ) {
147153 b -> m_data = b -> data_len ;
148154 kroundup32 (b -> m_data );
149- b -> data = (uint8_t * )realloc (b -> data , b -> m_data );
155+ b -> data = (uint8_t * )xrealloc (b -> data , b -> m_data );
150156 }
151157 if (bam_read (fp , b -> data , b -> data_len ) != b -> data_len ) return -4 ;
152158 b -> l_aux = b -> data_len - c -> n_cigar * 4 - c -> l_qname - c -> l_qseq - (c -> l_qseq + 1 )/2 ;
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