[med-svn] [Git][med-team/staden-io-lib][master] 6 commits: prepare for source only upload
Michael R. Crusoe
gitlab at salsa.debian.org
Thu May 21 09:50:51 BST 2020
Michael R. Crusoe pushed to branch master at Debian Med / staden-io-lib
Commits:
39c0b8ef by Michael R. Crusoe at 2020-05-21T10:39:24+02:00
prepare for source only upload
- - - - -
1744d492 by Michael R. Crusoe at 2020-05-21T10:49:47+02:00
install upstream's manual pages
- - - - -
d9d6a745 by Michael R. Crusoe at 2020-05-21T10:49:48+02:00
File more spelling typos
- - - - -
adf3d73d by Michael R. Crusoe at 2020-05-21T10:49:48+02:00
include symbols in the package
- - - - -
90e98227 by Michael R. Crusoe at 2020-05-21T10:49:48+02:00
debian/control: fix typo in the package descriptions
- - - - -
2205c1c5 by Michael R. Crusoe at 2020-05-21T10:49:48+02:00
debian/rules: add hack to autoconf not forget MMAP with cross building
- - - - -
6 changed files:
- debian/changelog
- debian/control
- + debian/libstaden-read14.symbols
- debian/patches/spelling
- debian/rules
- debian/staden-io-lib-utils.manpages
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+staden-io-lib (1.14.12-2) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * File more spelling typos
+ * Install upstream's manual pages
+ * include symbols in the package
+ * debian/control: fix typo in the package descriptions
+ * debian/rules: add hack to autoconf not forget MMAP with cross
+ building
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Thu, 21 May 2020 10:38:58 +0200
+
staden-io-lib (1.14.12-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -30,7 +30,7 @@ Description: programs for manipulating DNA sequencing files
.
This package contains the programs that are distributed with the Staden io_lib
for manipulating and converting sequencing data files, and in particular files
- to maniuplate short reads generated by second and third generation sequencers
+ to manipulate short reads generated by second and third generation sequencers
and stored in SRF format.
Package: libstaden-read-dev
@@ -77,7 +77,7 @@ Description: programs for manipulating DNA sequencing files (usage examples)
.
This package contains the programs that are distributed with the Staden io_lib
for manipulating and converting sequencing data files, and in particular files
- to maniuplate short reads generated by second and third generation sequencers
+ to manipulate short reads generated by second and third generation sequencers
and stored in SRF format.
.
This package contains example data and a test suite to test the data.
=====================================
debian/libstaden-read14.symbols
=====================================
@@ -0,0 +1,761 @@
+libstaden-read.so.14 libstaden-read14 #MINVER#
+* Build-Depends-Package: libstaden-read-dev
+ ArrayCreate at Base 1.14.12
+ ArrayDestroy at Base 1.14.12
+ ArrayError at Base 1.14.12
+ ArrayErrorString at Base 1.14.12
+ ArrayExtend at Base 1.14.12
+ ArrayRef at Base 1.14.12
+ Crc32Lookup at Base 1.14.12
+ HashFileCreate at Base 1.14.12
+ HashFileDestroy at Base 1.14.12
+ HashFileExtract at Base 1.14.12
+ HashFileFopen at Base 1.14.12
+ HashFileLoad at Base 1.14.12
+ HashFileOpen at Base 1.14.12
+ HashFileQuery at Base 1.14.12
+ HashFileSave at Base 1.14.12
+ HashHsieh at Base 1.14.12
+ HashJenkins3 at Base 1.14.12
+ HashJenkins at Base 1.14.12
+ HashTableAdd at Base 1.14.12
+ HashTableCreate at Base 1.14.12
+ HashTableDel at Base 1.14.12
+ HashTableDestroy at Base 1.14.12
+ HashTableDump at Base 1.14.12
+ HashTableIterCreate at Base 1.14.12
+ HashTableIterDestroy at Base 1.14.12
+ HashTableIterNext at Base 1.14.12
+ HashTableIterReset at Base 1.14.12
+ HashTableNext at Base 1.14.12
+ HashTableNextInt at Base 1.14.12
+ HashTableRemove at Base 1.14.12
+ HashTableResize at Base 1.14.12
+ HashTableSearch at Base 1.14.12
+ HashTableStats at Base 1.14.12
+ HashTcl at Base 1.14.12
+ MD5_Final at Base 1.14.12
+ MD5_Init at Base 1.14.12
+ MD5_Update at Base 1.14.12
+ abi_reset_data_counts at Base 1.14.12
+ abi_set_data_counts at Base 1.14.12
+ add_read_names at Base 1.14.12
+ append_int64 at Base 1.14.12
+ append_int at Base 1.14.12
+ append_uint at Base 1.14.12
+ bam_add_raw at Base 1.14.12
+ bam_aux_A at Base 1.14.12
+ bam_aux_Z at Base 1.14.12
+ bam_aux_add at Base 1.14.12
+ bam_aux_add_data at Base 1.14.12
+ bam_aux_add_from_sam at Base 1.14.12
+ bam_aux_add_vec at Base 1.14.12
+ bam_aux_d at Base 1.14.12
+ bam_aux_f at Base 1.14.12
+ bam_aux_find at Base 1.14.12
+ bam_aux_i at Base 1.14.12
+ bam_aux_iter at Base 1.14.12
+ bam_aux_iter_full at Base 1.14.12
+ bam_aux_size_vec at Base 1.14.12
+ bam_close at Base 1.14.12
+ bam_construct_seq at Base 1.14.12
+ bam_copy at Base 1.14.12
+ bam_dup at Base 1.14.12
+ bam_get_seq at Base 1.14.12
+ bam_next_seq at Base 1.14.12
+ bam_open at Base 1.14.12
+ bam_open_block at Base 1.14.12
+ bam_put_seq at Base 1.14.12
+ bam_set_option at Base 1.14.12
+ bam_set_voption at Base 1.14.12
+ bam_write_header at Base 1.14.12
+ be_read_int_1 at Base 1.14.12
+ be_read_int_2 at Base 1.14.12
+ be_read_int_4 at Base 1.14.12
+ be_read_int_8 at Base 1.14.12
+ be_write_int_1 at Base 1.14.12
+ be_write_int_2 at Base 1.14.12
+ be_write_int_4 at Base 1.14.12
+ be_write_int_8 at Base 1.14.12
+ bgzf_decode_thread at Base 1.14.12
+ bgzf_encode_thread at Base 1.14.12
+ bit_reverse at Base 1.14.12
+ block_create at Base 1.14.12
+ block_destroy at Base 1.14.12
+ block_resize at Base 1.14.12
+ bzi_close at Base 1.14.12
+ bzi_open at Base 1.14.12
+ bzi_read at Base 1.14.12
+ bzi_seek at Base 1.14.12
+ c2fstr at Base 1.14.12
+ calc_bit_lengths at Base 1.14.12
+ close_fofn at Base 1.14.12
+ codes2codeset at Base 1.14.12
+ compress_chunk at Base 1.14.12
+ compress_file at Base 1.14.12
+ compress_int2str at Base 1.14.12
+ compress_str2int at Base 1.14.12
+ compress_ztr at Base 1.14.12
+ compressed_file_exists at Base 1.14.12
+ conf2str at Base 1.14.12
+ construct_trace_name at Base 1.14.12
+ cram_allocate_encoder at Base 1.14.12
+ cram_beta_decode_char at Base 1.14.12
+ cram_beta_decode_free at Base 1.14.12
+ cram_beta_decode_init at Base 1.14.12
+ cram_beta_decode_int at Base 1.14.12
+ cram_beta_decode_long at Base 1.14.12
+ cram_beta_encode_char at Base 1.14.12
+ cram_beta_encode_free at Base 1.14.12
+ cram_beta_encode_init at Base 1.14.12
+ cram_beta_encode_int at Base 1.14.12
+ cram_beta_encode_long at Base 1.14.12
+ cram_beta_encode_store at Base 1.14.12
+ cram_block_method2str at Base 1.14.12
+ cram_byte_array_len_decode at Base 1.14.12
+ cram_byte_array_len_decode_free at Base 1.14.12
+ cram_byte_array_len_decode_init at Base 1.14.12
+ cram_byte_array_len_encode at Base 1.14.12
+ cram_byte_array_len_encode_free at Base 1.14.12
+ cram_byte_array_len_encode_init at Base 1.14.12
+ cram_byte_array_len_encode_store at Base 1.14.12
+ cram_byte_array_stop_decode_block at Base 1.14.12
+ cram_byte_array_stop_decode_free at Base 1.14.12
+ cram_byte_array_stop_decode_init at Base 1.14.12
+ cram_byte_array_stop_encode at Base 1.14.12
+ cram_byte_array_stop_encode_free at Base 1.14.12
+ cram_byte_array_stop_encode_init at Base 1.14.12
+ cram_byte_array_stop_encode_store at Base 1.14.12
+ cram_close at Base 1.14.12
+ cram_codec_decoder2encoder at Base 1.14.12
+ cram_codec_to_id at Base 1.14.12
+ cram_compress_block at Base 1.14.12
+ cram_content_type2str at Base 1.14.12
+ cram_deallocate_encoder at Base 1.14.12
+ cram_decode_TD at Base 1.14.12
+ cram_decode_compression_header at Base 1.14.12
+ cram_decode_estimate_sizes at Base 1.14.12
+ cram_decode_slice at Base 1.14.12
+ cram_decode_slice_header at Base 1.14.12
+ cram_decode_slice_mt at Base 1.14.12
+ cram_decode_slice_thread at Base 1.14.12
+ cram_decoder_init at Base 1.14.12
+ cram_default_version at Base 1.14.12
+ cram_dependent_data_series at Base 1.14.12
+ cram_encode_compression_header at Base 1.14.12
+ cram_encode_container at Base 1.14.12
+ cram_encode_slice_header at Base 1.14.12
+ cram_encoder_init at Base 1.14.12
+ cram_encoding2str at Base 1.14.12
+ cram_enque_compression_block at Base 1.14.12
+ cram_eof at Base 1.14.12
+ cram_external_decode_char at Base 1.14.12
+ cram_external_decode_free at Base 1.14.12
+ cram_external_decode_init at Base 1.14.12
+ cram_external_decode_int at Base 1.14.12
+ cram_external_decode_long at Base 1.14.12
+ cram_external_decode_sint at Base 1.14.12
+ cram_external_decode_size at Base 1.14.12
+ cram_external_decode_slong at Base 1.14.12
+ cram_external_encode_char at Base 1.14.12
+ cram_external_encode_free at Base 1.14.12
+ cram_external_encode_init at Base 1.14.12
+ cram_external_encode_int at Base 1.14.12
+ cram_external_encode_long at Base 1.14.12
+ cram_external_encode_sint at Base 1.14.12
+ cram_external_encode_slong at Base 1.14.12
+ cram_external_encode_store at Base 1.14.12
+ cram_external_get_block at Base 1.14.12
+ cram_flush at Base 1.14.12
+ cram_flush_container at Base 1.14.12
+ cram_flush_container_mt at Base 1.14.12
+ cram_flush_thread at Base 1.14.12
+ cram_free_block at Base 1.14.12
+ cram_free_compression_header at Base 1.14.12
+ cram_free_container at Base 1.14.12
+ cram_free_file_def at Base 1.14.12
+ cram_free_slice at Base 1.14.12
+ cram_free_slice_header at Base 1.14.12
+ cram_gamma_decode at Base 1.14.12
+ cram_gamma_decode_free at Base 1.14.12
+ cram_gamma_decode_init at Base 1.14.12
+ cram_get_bam_seq at Base 1.14.12
+ cram_get_ref at Base 1.14.12
+ cram_get_seq at Base 1.14.12
+ cram_huffman_decode_char0 at Base 1.14.12
+ cram_huffman_decode_char at Base 1.14.12
+ cram_huffman_decode_free at Base 1.14.12
+ cram_huffman_decode_init at Base 1.14.12
+ cram_huffman_decode_int0 at Base 1.14.12
+ cram_huffman_decode_int at Base 1.14.12
+ cram_huffman_decode_long0 at Base 1.14.12
+ cram_huffman_decode_long at Base 1.14.12
+ cram_huffman_decode_null at Base 1.14.12
+ cram_huffman_encode_char0 at Base 1.14.12
+ cram_huffman_encode_char at Base 1.14.12
+ cram_huffman_encode_free at Base 1.14.12
+ cram_huffman_encode_init at Base 1.14.12
+ cram_huffman_encode_int0 at Base 1.14.12
+ cram_huffman_encode_int at Base 1.14.12
+ cram_huffman_encode_long0 at Base 1.14.12
+ cram_huffman_encode_long at Base 1.14.12
+ cram_huffman_encode_store at Base 1.14.12
+ cram_index_build at Base 1.14.12
+ cram_index_free at Base 1.14.12
+ cram_index_load at Base 1.14.12
+ cram_index_load_via_callbacks at Base 1.14.12
+ cram_index_query at Base 1.14.12
+ cram_init_varint at Base 1.14.12
+ cram_io_allocate_output_buffer at Base 1.14.12
+ cram_io_close at Base 1.14.12
+ cram_io_deallocate_output_buffer at Base 1.14.12
+ cram_io_flush_output_buffer at Base 1.14.12
+ cram_io_input_buffer_fgets at Base 1.14.12
+ cram_io_input_buffer_read at Base 1.14.12
+ cram_io_input_buffer_seek at Base 1.14.12
+ cram_io_input_buffer_underflow at Base 1.14.12
+ cram_io_open at Base 1.14.12
+ cram_io_open_by_callbacks at Base 1.14.12
+ cram_io_openw_by_callbacks at Base 1.14.12
+ cram_io_output_buffer_putc at Base 1.14.12
+ cram_io_output_buffer_write at Base 1.14.12
+ cram_load_reference at Base 1.14.12
+ cram_mem_write_callback at Base 1.14.12
+ cram_new_block at Base 1.14.12
+ cram_new_compression_header at Base 1.14.12
+ cram_new_container at Base 1.14.12
+ cram_new_metrics at Base 1.14.12
+ cram_new_slice at Base 1.14.12
+ cram_nop_decode_reset at Base 1.14.12
+ cram_open at Base 1.14.12
+ cram_open_by_callbacks at Base 1.14.12
+ cram_openw_by_callbacks at Base 1.14.12
+ cram_process_work_package at Base 1.14.12
+ cram_put_bam_seq at Base 1.14.12
+ cram_read_SAM_hdr at Base 1.14.12
+ cram_read_block at Base 1.14.12
+ cram_read_container at Base 1.14.12
+ cram_read_file_def at Base 1.14.12
+ cram_read_slice at Base 1.14.12
+ cram_ref_decr at Base 1.14.12
+ cram_ref_incr at Base 1.14.12
+ cram_ref_load at Base 1.14.12
+ cram_seek at Base 1.14.12
+ cram_seek_to_refpos at Base 1.14.12
+ cram_set_option at Base 1.14.12
+ cram_set_voption at Base 1.14.12
+ cram_stats_add at Base 1.14.12
+ cram_stats_create at Base 1.14.12
+ cram_stats_del at Base 1.14.12
+ cram_stats_dump at Base 1.14.12
+ cram_stats_encoding at Base 1.14.12
+ cram_stats_free at Base 1.14.12
+ cram_stats_qual at Base 1.14.12
+ cram_subexp_decode at Base 1.14.12
+ cram_subexp_decode_free at Base 1.14.12
+ cram_subexp_decode_init at Base 1.14.12
+ cram_uncompress_block at Base 1.14.12
+ cram_update_curr_slice at Base 1.14.12
+ cram_write_SAM_hdr at Base 1.14.12
+ cram_write_block at Base 1.14.12
+ cram_write_container at Base 1.14.12
+ cram_write_eof_block at Base 1.14.12
+ cram_write_file_def at Base 1.14.12
+ cram_xdelta_decode_block at Base 1.14.12
+ cram_xdelta_decode_char at Base 1.14.12
+ cram_xdelta_decode_free at Base 1.14.12
+ cram_xdelta_decode_init at Base 1.14.12
+ cram_xdelta_decode_int at Base 1.14.12
+ cram_xdelta_decode_long at Base 1.14.12
+ cram_xdelta_decode_size at Base 1.14.12
+ cram_xdelta_encode_char at Base 1.14.12
+ cram_xdelta_encode_flush at Base 1.14.12
+ cram_xdelta_encode_free at Base 1.14.12
+ cram_xdelta_encode_init at Base 1.14.12
+ cram_xdelta_encode_int at Base 1.14.12
+ cram_xdelta_encode_long at Base 1.14.12
+ cram_xdelta_encode_store at Base 1.14.12
+ cram_xdelta_get_block at Base 1.14.12
+ cram_xpack_decode_char at Base 1.14.12
+ cram_xpack_decode_free at Base 1.14.12
+ cram_xpack_decode_init at Base 1.14.12
+ cram_xpack_decode_int at Base 1.14.12
+ cram_xpack_decode_long at Base 1.14.12
+ cram_xpack_decode_size at Base 1.14.12
+ cram_xpack_encode_char at Base 1.14.12
+ cram_xpack_encode_flush at Base 1.14.12
+ cram_xpack_encode_free at Base 1.14.12
+ cram_xpack_encode_init at Base 1.14.12
+ cram_xpack_encode_int at Base 1.14.12
+ cram_xpack_encode_long at Base 1.14.12
+ cram_xpack_encode_store at Base 1.14.12
+ cram_xpack_get_block at Base 1.14.12
+ cram_xrle_decode_char at Base 1.14.12
+ cram_xrle_decode_free at Base 1.14.12
+ cram_xrle_decode_init at Base 1.14.12
+ cram_xrle_decode_int at Base 1.14.12
+ cram_xrle_decode_long at Base 1.14.12
+ cram_xrle_decode_size at Base 1.14.12
+ cram_xrle_encode_char at Base 1.14.12
+ cram_xrle_encode_flush at Base 1.14.12
+ cram_xrle_encode_free at Base 1.14.12
+ cram_xrle_encode_init at Base 1.14.12
+ cram_xrle_encode_int at Base 1.14.12
+ cram_xrle_encode_long at Base 1.14.12
+ cram_xrle_encode_store at Base 1.14.12
+ cram_xrle_get_block at Base 1.14.12
+ crc32_16bytes at Base 1.14.12
+ decode_sff_common_header at Base 1.14.12
+ decode_sff_read_header at Base 1.14.12
+ decorrelate1 at Base 1.14.12
+ decorrelate1dyn at Base 1.14.12
+ decorrelate2 at Base 1.14.12
+ decorrelate2dyn at Base 1.14.12
+ decorrelate4 at Base 1.14.12
+ delete_ztr at Base 1.14.12
+ determine_trace_type at Base 1.14.12
+ dstring_append at Base 1.14.12
+ dstring_append_char at Base 1.14.12
+ dstring_append_hex_encoded at Base 1.14.12
+ dstring_append_int at Base 1.14.12
+ dstring_appendf at Base 1.14.12
+ dstring_create at Base 1.14.12
+ dstring_create_with at Base 1.14.12
+ dstring_delete at Base 1.14.12
+ dstring_destroy at Base 1.14.12
+ dstring_dinsert at Base 1.14.12
+ dstring_dreplace at Base 1.14.12
+ dstring_empty at Base 1.14.12
+ dstring_escape_html at Base 1.14.12
+ dstring_find at Base 1.14.12
+ dstring_find_replace at Base 1.14.12
+ dstring_find_replace_all at Base 1.14.12
+ dstring_htmlise_links at Base 1.14.12
+ dstring_insert at Base 1.14.12
+ dstring_insertf at Base 1.14.12
+ dstring_length at Base 1.14.12
+ dstring_nappend at Base 1.14.12
+ dstring_ninsert at Base 1.14.12
+ dstring_nprepend at Base 1.14.12
+ dstring_perror at Base 1.14.12
+ dstring_prepend at Base 1.14.12
+ dstring_prependf at Base 1.14.12
+ dstring_refresh_length at Base 1.14.12
+ dstring_replace at Base 1.14.12
+ dstring_resize at Base 1.14.12
+ dstring_str at Base 1.14.12
+ dstring_to_html at Base 1.14.12
+ dstring_vinsertf at Base 1.14.12
+ dump_labels at Base 1.14.12
+ eflt_feature_ids at Base 1.14.12
+ encode_sff_common_header at Base 1.14.12
+ encode_sff_read_header at Base 1.14.12
+ errout at Base 1.14.12
+ exp2read at Base 1.14.12
+ exp_close at Base 1.14.12
+ exp_create_info at Base 1.14.12
+ exp_create_range at Base 1.14.12
+ exp_destroy_info at Base 1.14.12
+ exp_extract_range at Base 1.14.12
+ exp_fread_info at Base 1.14.12
+ exp_get_feature_index at Base 1.14.12
+ exp_get_int at Base 1.14.12
+ exp_get_rng at Base 1.14.12
+ exp_get_str at Base 1.14.12
+ exp_mfread_info at Base 1.14.12
+ exp_print_file at Base 1.14.12
+ exp_print_line at Base 1.14.12
+ exp_print_mfile at Base 1.14.12
+ exp_print_mline at Base 1.14.12
+ exp_print_seq at Base 1.14.12
+ exp_put_int at Base 1.14.12
+ exp_put_rng at Base 1.14.12
+ exp_put_str at Base 1.14.12
+ exp_read_info at Base 1.14.12
+ exp_set_entry at Base 1.14.12
+ expand_8to16 at Base 1.14.12
+ expand_8to32 at Base 1.14.12
+ expand_cache_path at Base 1.14.12
+ expcr_ at Base 1.14.12
+ expected_template_count at Base 1.14.12
+ exper_ at Base 1.14.12
+ expkil_ at Base 1.14.12
+ expopn_ at Base 1.14.12
+ expri_ at Base 1.14.12
+ exprr_ at Base 1.14.12
+ exprs_ at Base 1.14.12
+ exprsa_ at Base 1.14.12
+ expwi_ at Base 1.14.12
+ expwr_ at Base 1.14.12
+ expws_ at Base 1.14.12
+ expwsa_ at Base 1.14.12
+ f2cstr at Base 1.14.12
+ fcompress_file at Base 1.14.12
+ fdetermine_trace_type at Base 1.14.12
+ file_exists at Base 1.14.12
+ file_size at Base 1.14.12
+ find_file_url at Base 1.14.12
+ flen at Base 1.14.12
+ follow1 at Base 1.14.12
+ fopen_compressed at Base 1.14.12
+ fread_abi at Base 1.14.12
+ fread_alf at Base 1.14.12
+ fread_pln at Base 1.14.12
+ fread_reading at Base 1.14.12
+ fread_scf at Base 1.14.12
+ fread_ztr at Base 1.14.12
+ free_sff_common_header at Base 1.14.12
+ free_sff_read_data at Base 1.14.12
+ free_sff_read_header at Base 1.14.12
+ freopen_compressed at Base 1.14.12
+ fstrlen at Base 1.14.12
+ fwrite_abi at Base 1.14.12
+ fwrite_alf at Base 1.14.12
+ fwrite_pln at Base 1.14.12
+ fwrite_reading at Base 1.14.12
+ fwrite_scf at Base 1.14.12
+ fwrite_ztr at Base 1.14.12
+ generate_code_set at Base 1.14.12
+ generate_consensus at Base 1.14.12
+ getABIIndexEntryLW at Base 1.14.12
+ getABIIndexEntrySW at Base 1.14.12
+ getABIIndexOffset at Base 1.14.12
+ getABIString at Base 1.14.12
+ getABIint1 at Base 1.14.12
+ getABIint2 at Base 1.14.12
+ getABIint4 at Base 1.14.12
+ get_compression_method at Base 1.14.12
+ get_read_conf at Base 1.14.12
+ gzi_index_add_block at Base 1.14.12
+ gzi_index_dump at Base 1.14.12
+ gzi_index_free at Base 1.14.12
+ gzi_index_init at Base 1.14.12
+ gzi_index_load at Base 1.14.12
+ gzi_load at Base 1.14.12
+ hash64 at Base 1.14.12
+ hash at Base 1.14.12
+ huffman_codes_destroy at Base 1.14.12
+ huffman_codeset_destroy at Base 1.14.12
+ huffman_decode at Base 1.14.12
+ huffman_multi_decode at Base 1.14.12
+ huffman_multi_encode at Base 1.14.12
+ ichebcomp at Base 1.14.12
+ ichebuncomp at Base 1.14.12
+ illumina_bin at Base 1.14.12
+ illumina_bin_33 at Base 1.14.12
+ init_decode_tables at Base 1.14.12
+ int32_decode at Base 1.14.12
+ int32_encode at Base 1.14.12
+ int32_get_blk at Base 1.14.12
+ int32_put at Base 1.14.12
+ int_to_float at Base 1.14.12
+ iolib_crc32 at Base 1.14.12
+ iolib_get_exp_path at Base 1.14.12
+ iolib_get_trace_path at Base 1.14.12
+ iolib_set_exp_path at Base 1.14.12
+ iolib_set_trace_path at Base 1.14.12
+ is_directory at Base 1.14.12
+ is_file at Base 1.14.12
+ is_scf at Base 1.14.12
+ itf8_bytes at Base 1.14.12
+ itf8_decode_crc at Base 1.14.12
+ itf8_put_blk at Base 1.14.12
+ itf8_size at Base 1.14.12
+ le_read_int_1 at Base 1.14.12
+ le_read_int_2 at Base 1.14.12
+ le_read_int_4 at Base 1.14.12
+ le_read_int_8 at Base 1.14.12
+ le_write_int_1 at Base 1.14.12
+ le_write_int_2 at Base 1.14.12
+ le_write_int_4 at Base 1.14.12
+ le_write_int_8 at Base 1.14.12
+ load_ref_portion at Base 1.14.12
+ log2_data at Base 1.14.12
+ lossy_read_names at Base 1.14.12
+ ltf8_bytes at Base 1.14.12
+ ltf8_decode at Base 1.14.12
+ ltf8_decode_crc at Base 1.14.12
+ ltf8_put_blk at Base 1.14.12
+ memgunzip at Base 1.14.12
+ memgzip at Base 1.14.12
+ mfascii at Base 1.14.12
+ mfclose at Base 1.14.12
+ mfcreate at Base 1.14.12
+ mfcreate_from at Base 1.14.12
+ mfdestroy at Base 1.14.12
+ mfdetach at Base 1.14.12
+ mfeof at Base 1.14.12
+ mfflush at Base 1.14.12
+ mfgetc at Base 1.14.12
+ mfgets at Base 1.14.12
+ mfmmap at Base 1.14.12
+ mfopen at Base 1.14.12
+ mfprintf at Base 1.14.12
+ mfread at Base 1.14.12
+ mfread_abi at Base 1.14.12
+ mfread_alf at Base 1.14.12
+ mfread_pln at Base 1.14.12
+ mfread_reading at Base 1.14.12
+ mfread_scf at Base 1.14.12
+ mfread_sff at Base 1.14.12
+ mfread_ztr at Base 1.14.12
+ mfrecreate at Base 1.14.12
+ mfreopen at Base 1.14.12
+ mfseek at Base 1.14.12
+ mfsteal at Base 1.14.12
+ mftell at Base 1.14.12
+ mftruncate at Base 1.14.12
+ mfwrite at Base 1.14.12
+ mfwrite_abi at Base 1.14.12
+ mfwrite_alf at Base 1.14.12
+ mfwrite_pln at Base 1.14.12
+ mfwrite_reading at Base 1.14.12
+ mfwrite_scf at Base 1.14.12
+ mfwrite_ztr at Base 1.14.12
+ mkdir_prefix at Base 1.14.12
+ mrewind at Base 1.14.12
+ mstderr at Base 1.14.12
+ mstdin at Base 1.14.12
+ mstdout at Base 1.14.12
+ mungetc at Base 1.14.12
+ myfind at Base 1.14.12
+ mystrtok at Base 1.14.12
+ new_ztr at Base 1.14.12
+ next_symbol at Base 1.14.12
+ open_exp_file at Base 1.14.12
+ open_exp_mfile at Base 1.14.12
+ open_fofn at Base 1.14.12
+ open_path_file at Base 1.14.12
+ open_path_mfile at Base 1.14.12
+ open_trace_file at Base 1.14.12
+ open_trace_mfile at Base 1.14.12
+ opos2str at Base 1.14.12
+ pack_trace_suffix at Base 1.14.12
+ paranoid_fclose at Base 1.14.12
+ partial_decode_ztr at Base 1.14.12
+ pool_alloc at Base 1.14.12
+ pool_create at Base 1.14.12
+ pool_destroy at Base 1.14.12
+ pool_free at Base 1.14.12
+ qshift at Base 1.14.12
+ read2exp at Base 1.14.12
+ read2scf at Base 1.14.12
+ read2ztr at Base 1.14.12
+ read_abi at Base 1.14.12
+ read_alf at Base 1.14.12
+ read_allocate at Base 1.14.12
+ read_deallocate at Base 1.14.12
+ read_dup at Base 1.14.12
+ read_experiment_redirect at Base 1.14.12
+ read_fofn at Base 1.14.12
+ read_pln at Base 1.14.12
+ read_reading at Base 1.14.12
+ read_scf at Base 1.14.12
+ read_scf_base at Base 1.14.12
+ read_scf_bases3 at Base 1.14.12
+ read_scf_bases at Base 1.14.12
+ read_scf_comment at Base 1.14.12
+ read_scf_header at Base 1.14.12
+ read_scf_sample1 at Base 1.14.12
+ read_scf_sample2 at Base 1.14.12
+ read_scf_samples1 at Base 1.14.12
+ read_scf_samples2 at Base 1.14.12
+ read_scf_samples31 at Base 1.14.12
+ read_scf_samples32 at Base 1.14.12
+ read_sections at Base 1.14.12
+ read_sff_common_header at Base 1.14.12
+ read_sff_read_data at Base 1.14.12
+ read_sff_read_header at Base 1.14.12
+ read_update_base_positions at Base 1.14.12
+ read_update_confidence_values at Base 1.14.12
+ recorrelate1 at Base 1.14.12
+ recorrelate2 at Base 1.14.12
+ recorrelate4 at Base 1.14.12
+ refs2id at Base 1.14.12
+ refs_free at Base 1.14.12
+ refs_load_fai at Base 1.14.12
+ remove_extension at Base 1.14.12
+ remove_file at Base 1.14.12
+ reset_metrics at Base 1.14.12
+ restore_codes at Base 1.14.12
+ restore_codes_single at Base 1.14.12
+ rle at Base 1.14.12
+ safe_itf8_put at Base 1.14.12
+ safe_ltf8_put at Base 1.14.12
+ sam_hdr_PG_ID at Base 1.14.12
+ sam_hdr_add at Base 1.14.12
+ sam_hdr_add_PG at Base 1.14.12
+ sam_hdr_add_lines at Base 1.14.12
+ sam_hdr_decr_ref at Base 1.14.12
+ sam_hdr_dump at Base 1.14.12
+ sam_hdr_dup at Base 1.14.12
+ sam_hdr_find at Base 1.14.12
+ sam_hdr_find_key at Base 1.14.12
+ sam_hdr_find_line at Base 1.14.12
+ sam_hdr_find_rg at Base 1.14.12
+ sam_hdr_free at Base 1.14.12
+ sam_hdr_incr_ref at Base 1.14.12
+ sam_hdr_length at Base 1.14.12
+ sam_hdr_link_pg at Base 1.14.12
+ sam_hdr_name2ref at Base 1.14.12
+ sam_hdr_new at Base 1.14.12
+ sam_hdr_parse at Base 1.14.12
+ sam_hdr_rebuild at Base 1.14.12
+ sam_hdr_sort_order at Base 1.14.12
+ sam_hdr_str at Base 1.14.12
+ sam_hdr_update at Base 1.14.12
+ sam_hdr_vadd at Base 1.14.12
+ scf2read at Base 1.14.12
+ scf_allocate at Base 1.14.12
+ scf_deallocate at Base 1.14.12
+ scf_delta_samples1 at Base 1.14.12
+ scf_delta_samples2 at Base 1.14.12
+ scf_version_float2str at Base 1.14.12
+ scf_version_str2float at Base 1.14.12
+ scram_close at Base 1.14.12
+ scram_get_header at Base 1.14.12
+ scram_get_refs at Base 1.14.12
+ scram_get_seq at Base 1.14.12
+ scram_init at Base 1.14.12
+ scram_input_bam_block at Base 1.14.12
+ scram_line at Base 1.14.12
+ scram_next_seq at Base 1.14.12
+ scram_open at Base 1.14.12
+ scram_open_cram_via_callbacks at Base 1.14.12
+ scram_put_seq at Base 1.14.12
+ scram_set_header at Base 1.14.12
+ scram_set_option at Base 1.14.12
+ scram_set_refs at Base 1.14.12
+ scram_write_header at Base 1.14.12
+ set_compression_method at Base 1.14.12
+ set_scf_version at Base 1.14.12
+ shrink_16to8 at Base 1.14.12
+ shrink_32to8 at Base 1.14.12
+ srf_construct_cont_hdr at Base 1.14.12
+ srf_construct_trace_body at Base 1.14.12
+ srf_construct_trace_hdr at Base 1.14.12
+ srf_create at Base 1.14.12
+ srf_destroy at Base 1.14.12
+ srf_destroy_cont_hdr at Base 1.14.12
+ srf_destroy_trace_body at Base 1.14.12
+ srf_destroy_trace_hdr at Base 1.14.12
+ srf_find_trace at Base 1.14.12
+ srf_index_add_cont_hdr at Base 1.14.12
+ srf_index_add_trace_body at Base 1.14.12
+ srf_index_add_trace_hdr at Base 1.14.12
+ srf_index_create at Base 1.14.12
+ srf_index_destroy at Base 1.14.12
+ srf_index_stats at Base 1.14.12
+ srf_index_write at Base 1.14.12
+ srf_next_block_details at Base 1.14.12
+ srf_next_block_type at Base 1.14.12
+ srf_next_trace at Base 1.14.12
+ srf_next_ztr at Base 1.14.12
+ srf_next_ztr_flags at Base 1.14.12
+ srf_open at Base 1.14.12
+ srf_read_cont_hdr at Base 1.14.12
+ srf_read_index_hdr at Base 1.14.12
+ srf_read_pstring at Base 1.14.12
+ srf_read_trace_body at Base 1.14.12
+ srf_read_trace_hdr at Base 1.14.12
+ srf_read_uint32 at Base 1.14.12
+ srf_read_uint64 at Base 1.14.12
+ srf_read_xml at Base 1.14.12
+ srf_write_cont_hdr at Base 1.14.12
+ srf_write_index_hdr at Base 1.14.12
+ srf_write_pstring at Base 1.14.12
+ srf_write_pstringb at Base 1.14.12
+ srf_write_trace_body at Base 1.14.12
+ srf_write_trace_hdr at Base 1.14.12
+ srf_write_uint32 at Base 1.14.12
+ srf_write_uint64 at Base 1.14.12
+ srf_write_xml at Base 1.14.12
+ sthuff at Base 1.14.12
+ store_bytes at Base 1.14.12
+ store_codes at Base 1.14.12
+ store_codes_single at Base 1.14.12
+ str2conf at Base 1.14.12
+ str2opos at Base 1.14.12
+ str_tolower at Base 1.14.12
+ str_toupper at Base 1.14.12
+ string_alloc at Base 1.14.12
+ string_dup at Base 1.14.12
+ string_ndup at Base 1.14.12
+ string_pool_create at Base 1.14.12
+ string_pool_destroy at Base 1.14.12
+ stringify_argv at Base 1.14.12
+ t_pool_delete_result at Base 1.14.12
+ t_pool_destroy at Base 1.14.12
+ t_pool_dispatch2 at Base 1.14.12
+ t_pool_dispatch at Base 1.14.12
+ t_pool_flush at Base 1.14.12
+ t_pool_init at Base 1.14.12
+ t_pool_next_result at Base 1.14.12
+ t_pool_next_result_wait at Base 1.14.12
+ t_pool_results_queue_empty at Base 1.14.12
+ t_pool_results_queue_len at Base 1.14.12
+ t_pool_results_queue_sz at Base 1.14.12
+ t_results_queue_destroy at Base 1.14.12
+ t_results_queue_init at Base 1.14.12
+ tokenise_search_path at Base 1.14.12
+ trace_type_int2str at Base 1.14.12
+ trace_type_str2int at Base 1.14.12
+ trace_type_str at Base 1.14.12
+ tshift at Base 1.14.12
+ uncompress_chunk at Base 1.14.12
+ uncompress_ztr at Base 1.14.12
+ unfollow1 at Base 1.14.12
+ unlog2_data at Base 1.14.12
+ unqshift at Base 1.14.12
+ unrle at Base 1.14.12
+ unsthuff at Base 1.14.12
+ untshift at Base 1.14.12
+ unxrle2 at Base 1.14.12
+ unxrle at Base 1.14.12
+ vflen at Base 1.14.12
+ write_abi at Base 1.14.12
+ write_alf at Base 1.14.12
+ write_pln at Base 1.14.12
+ write_reading at Base 1.14.12
+ write_scf at Base 1.14.12
+ write_scf_base at Base 1.14.12
+ write_scf_bases3 at Base 1.14.12
+ write_scf_bases at Base 1.14.12
+ write_scf_comment at Base 1.14.12
+ write_scf_header at Base 1.14.12
+ write_scf_sample1 at Base 1.14.12
+ write_scf_sample2 at Base 1.14.12
+ write_scf_samples1 at Base 1.14.12
+ write_scf_samples2 at Base 1.14.12
+ write_scf_samples31 at Base 1.14.12
+ write_scf_samples32 at Base 1.14.12
+ xcalloc at Base 1.14.12
+ xfree at Base 1.14.12
+ xmalloc at Base 1.14.12
+ xrealloc at Base 1.14.12
+ xrle2 at Base 1.14.12
+ xrle at Base 1.14.12
+ zfclose at Base 1.14.12
+ zfeof at Base 1.14.12
+ zfgets at Base 1.14.12
+ zfopen at Base 1.14.12
+ zfpeek at Base 1.14.12
+ zfputs at Base 1.14.12
+ zfseeko at Base 1.14.12
+ zftello at Base 1.14.12
+ zlib_dehuff at Base 1.14.12
+ zlib_huff at Base 1.14.12
+ zlib_mem_inflate at Base 1.14.12
+ ztr2read at Base 1.14.12
+ ztr_add_hcode at Base 1.14.12
+ ztr_add_text at Base 1.14.12
+ ztr_dup at Base 1.14.12
+ ztr_find_chunks at Base 1.14.12
+ ztr_find_hcode at Base 1.14.12
+ ztr_find_hcode_chunk at Base 1.14.12
+ ztr_lookup_mdata_value at Base 1.14.12
+ ztr_new_chunk at Base 1.14.12
+ ztr_process_text at Base 1.14.12
+ ztr_read_chunk_hdr at Base 1.14.12
+ ztr_read_header at Base 1.14.12
+ ztr_store_hcodes at Base 1.14.12
=====================================
debian/patches/spelling
=====================================
@@ -44,3 +44,83 @@ Subject: Spelling: independant→independent
* 25.11.91 SD There was a hard limit (of 1024) for allocation of
* space for number of bases, yet program would
* read in more if there were any, causing nasties to happen.
+--- staden-io-lib.orig/progs/srf2fastq.c
++++ staden-io-lib/progs/srf2fastq.c
+@@ -641,7 +641,7 @@
+
+ if ( reverse_set && ! (sequential || split) ) {
+ fprintf(stderr, "ERROR: The -r parameter is only supported when "
+- "spliting sequences by region.\n");
++ "splitting sequences by region.\n");
+ usage();
+ }
+
+--- staden-io-lib.orig/io_lib/bam.c
++++ staden-io-lib/io_lib/bam.c
+@@ -3680,7 +3680,7 @@
+ }
+
+ default:
+- fprintf(stderr, "Unhandled auxilary type '%c' in "
++ fprintf(stderr, "Unhandled auxiliary type '%c' in "
+ "bam_put_seq()\n", type);
+ }
+ }
+--- staden-io-lib.orig/io_lib/compression.c
++++ staden-io-lib/io_lib/compression.c
+@@ -139,7 +139,7 @@
+ zstr.opaque = (voidpf)0;
+
+ if ((err = deflateInit2(&zstr, 1, Z_DEFLATED, 15, 8, strategy)) != Z_OK) {
+- fprintf(stderr, "zlib errror in deflateInit2(): %d\n", err);
++ fprintf(stderr, "zlib error in deflateInit2(): %d\n", err);
+ return NULL;
+ }
+
+@@ -151,7 +151,7 @@
+
+ /* Do the compression */
+ if ((err = deflate(&zstr, Z_FINISH)) != Z_STREAM_END) {
+- fprintf(stderr, "zlib errror in deflate(): %d\n", err);
++ fprintf(stderr, "zlib error in deflate(): %d\n", err);
+ return NULL;
+ }
+
+@@ -207,7 +207,7 @@
+ zstr.opaque = (voidpf)0;
+
+ if ((err = inflateInit(&zstr)) != Z_OK) {
+- fprintf(stderr, "zlib errror in inflateInit(): %d\n", err);
++ fprintf(stderr, "zlib error in inflateInit(): %d\n", err);
+ return NULL;
+ }
+
+@@ -219,7 +219,7 @@
+
+ /* Do the decompression */
+ if ((err = inflate(&zstr, Z_FINISH)) != Z_STREAM_END) {
+- fprintf(stderr, "zlib errror in deflate(): %d\n", err);
++ fprintf(stderr, "zlib error in deflate(): %d\n", err);
+ return NULL;
+ }
+
+--- staden-io-lib.orig/progs/scramble.c
++++ staden-io-lib/progs/scramble.c
+@@ -488,7 +488,7 @@
+ if (embed_ref) {
+ if (scram_get_header(in)->sort_order == ORDER_NAME ||
+ scram_get_header(in)->sort_order == ORDER_UNSORTED) {
+- fprintf(stderr, "Embeded reference with non-coordinate sorted data is "
++ fprintf(stderr, "Embedded reference with non-coordinate sorted data is "
+ "not supported.\nUsing -x for no-ref instead.\n");
+ if (scram_set_option(out, CRAM_OPT_NO_REF, 1))
+ return 1;
+@@ -501,7 +501,7 @@
+ if (embed_cons) {
+ if (scram_get_header(in)->sort_order == ORDER_NAME ||
+ scram_get_header(in)->sort_order == ORDER_UNSORTED) {
+- fprintf(stderr, "Embeded consensus with non-coordinate sorted data is "
++ fprintf(stderr, "Embedded consensus with non-coordinate sorted data is "
+ "not supported.\n");
+ } else {
+ if (scram_set_option(out, CRAM_OPT_EMBED_CONS, embed_cons))
=====================================
debian/rules
=====================================
@@ -16,6 +16,9 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
%:
dh $@ --no-parallel
+override_dh_auto_configure:
+ export ac_cv_func_mmap_fixed_mapped=yes && dh_auto_configure
+
override_dh_install-arch:
dh_install -a
mkdir -p $(CURDIR)/debian/$(devpkg)/usr/bin
@@ -33,15 +36,6 @@ override_dh_install-arch:
# make sure io_lib-config --libs will not return -pie (see #825461)
find debian/*/usr/bin -name io_lib-config -exec sed -i -e 's/ *-fPIE//' -e 's/ *-pie//' \{\} \;
-#override_dh_installman:
- #dh_installman
- # manpages need some post editing but in case it could be automated, this code would help
- # mkdir -p $(mandir)
- # help2man --no-discard-stderr --no-info --help-option='""' \
- # --name='filter SRF files for various purposes' \
- # --version-string="$(version)" \
- # $(CURDIR)/debian/$(utils)/usr/bin/srf_filter > $(mandir)/srf_filter.1
-
override_dh_install-indep:
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
echo "Do not run test suite for architecture independent builds"
=====================================
debian/staden-io-lib-utils.manpages
=====================================
@@ -1,2 +1,2 @@
-man/man1/*1
+usr/share/man/man1/*
debian/man1/*.1
View it on GitLab: https://salsa.debian.org/med-team/staden-io-lib/-/compare/b27ab65ff3033e3a02a0ade35ab5e4c1e33ae765...2205c1c5418af487d7303068e4d78c51aad821dd
--
View it on GitLab: https://salsa.debian.org/med-team/staden-io-lib/-/compare/b27ab65ff3033e3a02a0ade35ab5e4c1e33ae765...2205c1c5418af487d7303068e4d78c51aad821dd
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