int subsample(int nseqs, char *fastqfile, struct fastq *seqs[], int compressed) {
// read the fastq file into a temporary hash
struct fastq *allseqs[HASHSIZE] = {NULL};
int read_seqs = 0;
if (compressed)
read_seqs = read_fastq_gz(fastqfile, allseqs);
else
read_seqs = read_fastq(fastqfile, allseqs);
if (read_seqs < nseqs) {
fprintf(stderr, "You requested %d sequences but there are only %d in the file!\n", nseqs, read_seqs);
nseqs = read_seqs;
}
// get all the ids from the sequences
char *ids[read_seqs];
get_ids(ids, allseqs);
// subsample those IDs
char **subsample = subsample_n(read_seqs, ids, nseqs);
for (int i=0; i<nseqs; i++) {
char *info = get_seq_information(subsample[i], seqs);
char *seq = get_sequence(subsample[i], seqs);
char *qua = get_quality(subsample[i], seqs);
}
return nseqs;
}
int parse_command(int argc, char *argv[], option_t* opt)
{
int i;
for (i =1; i < argc; i++)
{
if (strcmp(argv[i], "-rel") == 0)
{
if (0 > get_resolution(atoi(argv[++i]), &opt->width, &opt->height))
return -1;
}
else if (strcmp(argv[i], "-q") == 0)
{
opt->quality = get_quality(atoi(argv[++i]));
}
else if (strcmp(argv[i], "-w") == 0)
{
opt->white_balance = atoi(argv[++i]);
}
else if (strcmp(argv[i], "-s") == 0)
{
opt->sharpness = atoi(argv[++i]);
}
else if (strcmp(argv[i], "-iso") == 0)
{
opt->iso = atoi(argv[++i]);
}
else if (strcmp(argv[i], "-ev") == 0)
{
opt->ev = atoi(argv[++i]);
}
else if (strcmp(argv[i], "-c") == 0)
{
opt->color = atoi(argv[++i]);
}
else if (strcmp(argv[i], "-timestamp") == 0)
{
opt->time_stamp = atoi(argv[++i]);
}
else if (strcmp(argv[i], "-o") == 0)
{
strcpy(opt->outpath, argv[++i]);
printf("outpath = %s\n", opt->outpath);
}
else if (strcmp(argv[i], "-seq") == 0)
{
opt->sequence = atoi(argv[++i]);
printf("sequence = %d\n", opt->sequence);
}
}
return 0;
}
void
test_iou_to_iou ()
{
testcase ("IOU to IOU");
Quality q1 = get_quality ("1", "1");
// Highly exaggerated 50% transfer rate for the input and output:
Rate const rate { parityRate.value + (parityRate.value / 2) };
// TAKER OWNER
// QUAL OFFER FUNDS QUAL OFFER FUNDS EXPECTED
// EUR USD
attempt (Sell, "N:N", q1, { "2", "2" }, "10", q1, { "2", "2" }, "10", { "2", "2" }, eur(), usd(), rate, rate);
attempt (Sell, "N:B", q1, { "4", "4" }, "10", q1, { "4", "4" }, "4", { "2.666666666666666", "2.666666666666666" }, eur(), usd(), rate, rate);
attempt (Buy, "N:T", q1, { "1", "1" }, "10", q1, { "2", "2" }, "10", { "1", "1" }, eur(), usd(), rate, rate);
attempt (Buy, "N:BT", q1, { "2", "2" }, "10", q1, { "6", "6" }, "5", { "2", "2" }, eur(), usd(), rate, rate);
attempt (Buy, "N:TB", q1, { "2", "2" }, "2", q1, { "6", "6" }, "1", { "0.6666666666666667", "0.6666666666666667" }, eur(), usd(), rate, rate);
attempt (Sell, "A:N", q1, { "2", "2" }, "2.5", q1, { "2", "2" }, "10", { "1.666666666666666", "1.666666666666666" }, eur(), usd(), rate, rate);
}
void
test_iou_to_xrp ()
{
testcase ("XRP Quantization: output");
Quality q1 = get_quality ("1", "1");
// TAKER OWNER
// QUAL OFFER FUNDS QUAL OFFER FUNDS EXPECTED
// USD XRP
attempt (Sell, "N:N", q1, { "3", "3" }, "3", q1, { "3", "3" }, "3", { "3", "3" }, usd(), xrp());
attempt (Sell, "N:B", q1, { "3", "3" }, "3", q1, { "3", "3" }, "2", { "2", "2" }, usd(), xrp());
attempt (Buy, "N:T", q1, { "3", "3" }, "2.5", q1, { "5", "5" }, "5", { "2.5", "2" }, usd(), xrp());
attempt (Buy, "N:BT", q1, { "3", "3" }, "1.5", q1, { "5", "5" }, "4", { "1.5", "1" }, usd(), xrp());
attempt (Buy, "N:TB", q1, { "3", "3" }, "2.2", q1, { "5", "5" }, "1", { "1", "1" }, usd(), xrp());
attempt (Sell, "T:N", q1, { "1", "1" }, "2", q1, { "2", "2" }, "2", { "1", "1" }, usd(), xrp());
attempt (Sell, "T:B", q1, { "2", "2" }, "2", q1, { "3", "3" }, "1", { "1", "1" }, usd(), xrp());
attempt (Buy, "T:T", q1, { "1", "1" }, "2", q1, { "2", "2" }, "2", { "1", "1" }, usd(), xrp());
attempt (Buy, "T:BT", q1, { "1", "1" }, "2", q1, { "3", "3" }, "2", { "1", "1" }, usd(), xrp());
attempt (Buy, "T:TB", q1, { "2", "2" }, "2", q1, { "3", "3" }, "1", { "1", "1" }, usd(), xrp());
attempt (Sell, "A:N", q1, { "2", "2" }, "1.5", q1, { "2", "2" }, "2", { "1.5", "1" }, usd(), xrp());
attempt (Sell, "A:B", q1, { "2", "2" }, "1.8", q1, { "3", "3" }, "2", { "1.8", "1" }, usd(), xrp());
attempt (Buy, "A:T", q1, { "2", "2" }, "1.2", q1, { "3", "3" }, "3", { "1.2", "1" }, usd(), xrp());
attempt (Buy, "A:BT", q1, { "2", "2" }, "1.5", q1, { "4", "4" }, "3", { "1.5", "1" }, usd(), xrp());
attempt (Buy, "A:TB", q1, { "2", "2" }, "1.5", q1, { "4", "4" }, "1", { "1", "1" }, usd(), xrp());
attempt (Sell, "TA:N", q1, { "2", "2" }, "1.5", q1, { "2", "2" }, "2", { "1.5", "1" }, usd(), xrp());
attempt (Sell, "TA:B", q1, { "2", "2" }, "1.5", q1, { "3", "3" }, "1", { "1", "1" }, usd(), xrp());
attempt (Buy, "TA:T", q1, { "2", "2" }, "1.5", q1, { "3", "3" }, "3", { "1.5", "1" }, usd(), xrp());
attempt (Buy, "TA:BT", q1, { "2", "2" }, "1.8", q1, { "4", "4" }, "3", { "1.8", "1" }, usd(), xrp());
attempt (Buy, "TA:TB", q1, { "2", "2" }, "1.2", q1, { "3", "3" }, "1", { "1", "1" }, usd(), xrp());
attempt (Sell, "AT:N", q1, { "2", "2" }, "2.5", q1, { "4", "4" }, "4", { "2", "2" }, usd(), xrp());
attempt (Sell, "AT:B", q1, { "2", "2" }, "2.5", q1, { "3", "3" }, "1", { "1", "1" }, usd(), xrp());
attempt (Buy, "AT:T", q1, { "2", "2" }, "2.5", q1, { "3", "3" }, "3", { "2", "2" }, usd(), xrp());
attempt (Buy, "AT:BT", q1, { "2", "2" }, "2.5", q1, { "4", "4" }, "3", { "2", "2" }, usd(), xrp());
attempt (Buy, "AT:TB", q1, { "2", "2" }, "2.5", q1, { "3", "3" }, "1", { "1", "1" }, usd(), xrp());
}
// NIKB TODO: Augment TestTaker so currencies and rates can be specified
// once without need for repetition.
void
test_xrp_to_iou ()
{
testcase ("XRP Quantization: input");
Quality q1 = get_quality ("1", "1");
// TAKER OWNER
// QUAL OFFER FUNDS QUAL OFFER FUNDS EXPECTED
// XRP USD
attempt (Sell, "N:N", q1, { "2", "2" }, "2", q1, { "2", "2" }, "2", { "2", "2" }, xrp(), usd());
attempt (Sell, "N:B", q1, { "2", "2" }, "2", q1, { "2", "2" }, "1.8", { "1", "1.8" }, xrp(), usd());
attempt (Buy, "N:T", q1, { "1", "1" }, "2", q1, { "2", "2" }, "2", { "1", "1" }, xrp(), usd());
attempt (Buy, "N:BT", q1, { "1", "1" }, "2", q1, { "2", "2" }, "1.8", { "1", "1" }, xrp(), usd());
attempt (Buy, "N:TB", q1, { "1", "1" }, "2", q1, { "2", "2" }, "0.8", { "0", "0.8" }, xrp(), usd());
attempt (Sell, "T:N", q1, { "1", "1" }, "2", q1, { "2", "2" }, "2", { "1", "1" }, xrp(), usd());
attempt (Sell, "T:B", q1, { "1", "1" }, "2", q1, { "2", "2" }, "1.8", { "1", "1.8" }, xrp(), usd());
attempt (Buy, "T:T", q1, { "1", "1" }, "2", q1, { "2", "2" }, "2", { "1", "1" }, xrp(), usd());
attempt (Buy, "T:BT", q1, { "1", "1" }, "2", q1, { "2", "2" }, "1.8", { "1", "1" }, xrp(), usd());
attempt (Buy, "T:TB", q1, { "1", "1" }, "2", q1, { "2", "2" }, "0.8", { "0", "0.8" }, xrp(), usd());
attempt (Sell, "A:N", q1, { "2", "2" }, "1", q1, { "2", "2" }, "2", { "1", "1" }, xrp(), usd());
attempt (Sell, "A:B", q1, { "2", "2" }, "1", q1, { "2", "2" }, "1.8", { "1", "1.8" }, xrp(), usd());
attempt (Buy, "A:T", q1, { "2", "2" }, "1", q1, { "3", "3" }, "3", { "1", "1" }, xrp(), usd());
attempt (Buy, "A:BT", q1, { "2", "2" }, "1", q1, { "3", "3" }, "2.4", { "1", "1" }, xrp(), usd());
attempt (Buy, "A:TB", q1, { "2", "2" }, "1", q1, { "3", "3" }, "0.8", { "0", "0.8" }, xrp(), usd());
attempt (Sell, "TA:N", q1, { "2", "2" }, "1", q1, { "2", "2" }, "2", { "1", "1" }, xrp(), usd());
attempt (Sell, "TA:B", q1, { "2", "2" }, "1", q1, { "3", "3" }, "1.8", { "1", "1.8" }, xrp(), usd());
attempt (Buy, "TA:T", q1, { "2", "2" }, "1", q1, { "3", "3" }, "3", { "1", "1" }, xrp(), usd());
attempt (Buy, "TA:BT", q1, { "2", "2" }, "1", q1, { "3", "3" }, "1.8", { "1", "1.8" }, xrp(), usd());
attempt (Buy, "TA:TB", q1, { "2", "2" }, "1", q1, { "3", "3" }, "1.8", { "1", "1.8" }, xrp(), usd());
attempt (Sell, "AT:N", q1, { "2", "2" }, "1", q1, { "3", "3" }, "3", { "1", "1" }, xrp(), usd());
attempt (Sell, "AT:B", q1, { "2", "2" }, "1", q1, { "3", "3" }, "1.8", { "1", "1.8" }, xrp(), usd());
attempt (Buy, "AT:T", q1, { "2", "2" }, "1", q1, { "3", "3" }, "3", { "1", "1" }, xrp(), usd());
attempt (Buy, "AT:BT", q1, { "2", "2" }, "1", q1, { "3", "3" }, "1.8", { "1", "1.8" }, xrp(), usd());
attempt (Buy, "AT:TB", q1, { "2", "2" }, "1", q1, { "3", "3" }, "0.8", { "0", "0.8" }, xrp(), usd());
}
/*
* process one BAM record, and store accumulated results in 'results'
*/
int seqchksum_processRecord(bam1_t *rec, HASH_TYPE hash, chksum_results_t *results)
{
uint32_t crc = 0;
uint16_t aflags = rec->core.flag;
uint8_t *seq = get_read(rec);
uint8_t *qual = get_quality(rec);
uint16_t flag_mask = BAM_FPAIRED | BAM_FREAD1 | BAM_FREAD2;
uint8_t flags = (aflags & flag_mask) & 0xFF;
bool pass = !(aflags & BAM_FQCFAIL);;
char *qname = bam_get_qname(rec);
uint8_t *tag;
char *rgid;
HashItem *hi;
HashData hd;
int newitem;
digest_line_t *dline_all;
digest_line_t *dline;
// look up the RG tag
tag = bam_aux_get(rec, "RG");
//hd.p = malloc(sizeof(digest_line_t));
if (tag) rgid = bam_aux2Z(tag);
else rgid = "";
hd.p = NULL;
hi = HashTableAdd(results->rgHash, rgid, 0, hd, &newitem);
if (newitem) {
hi->data.p = malloc(sizeof(digest_line_t));
dline = hi->data.p;
init_digest_line(hash,dline);
} else {
dline = hi->data.p;
}
dline_all = &(results->all);
// flags + sequence chksum
update_crc(&crc,&flags,1);
update_crc(&crc,seq,strlen((char*)seq));
update_digest_line(hash, pass, dline, crc, 0);
update_digest_line(hash, pass, dline_all, crc, 0);
// flags + sequence + quality chksum (don't reset crc, just add quality)
update_crc(&crc,qual,strlen((char*)qual));
update_digest_line(hash, pass, dline, crc, 2);
update_digest_line(hash, pass, dline_all, crc, 2);
// name + flags + sequence chksum
crc = 0;
update_crc(&crc, (uint8_t *)qname, strlen(qname)+1);
update_crc(&crc, &flags, 1);
update_crc(&crc,seq,strlen((char*)seq));
update_digest_line(hash, pass, dline, crc, 1);
update_digest_line(hash, pass, dline_all, crc, 1);
// flags + sequence + tags chksum
crc = 0;
update_crc(&crc, &flags, 1);
update_crc(&crc,seq,strlen((char*)seq));
tag = bam_aux_get(rec,"BC"); if (tag) update_crc(&crc,tag-2,aux_type2size(tag)+3);
tag = bam_aux_get(rec,"FI"); if (tag) update_crc(&crc,tag-2,aux_type2size(tag)+3);
tag = bam_aux_get(rec,"QT"); if (tag) update_crc(&crc,tag-2,aux_type2size(tag)+3);
tag = bam_aux_get(rec,"RT"); if (tag) update_crc(&crc,tag-2,aux_type2size(tag)+3);
tag = bam_aux_get(rec,"TC"); if (tag) update_crc(&crc,tag-2,aux_type2size(tag)+3);
update_digest_line(hash, pass, dline, crc, 3);
update_digest_line(hash, pass, dline_all, crc, 3);
free(seq); free(qual);
return 0;
}
int main(int argc, char *argv[]) {
// this file has 5 sequences in it so it should be easy to read!
char *filename = "../example_data/small.fastq.gz";
struct fastq *seqs[HASHSIZE] = {NULL};
int nseqs = read_fastq_gz(filename, seqs);
int error = 0;
if (nseqs != ESEQS) {
fprintf(stderr, "There was an error reading %s. We retrieved %d sequences but should have found %d sequences\n", filename, nseqs, ESEQS);
error = 1;
}
/* now test the get sequence methods */
int nnseqs = number_of_sequences(seqs);
if (nnseqs != ESEQS) {
printf("There was an error checking the number of sequences. We found %d using number_of_sequences but it should be %d\n", nnseqs, ESEQS);
error++;
}
/* test getting the ids */
char *ids[nnseqs];
int nnseqsids = get_ids(ids, seqs);
if (nnseqsids != nnseqs) {
printf("There was an error when we got the ids. This returned %d ids but it should be %d\n", nnseqsids, nnseqs);
error++;
}
printf("Got %d ids\n", nnseqsids);
for (int i=0; i<nnseqsids; i++)
printf("ID %d: %s\n", i, ids[i]);
char *sq = get_sequence("@GFH7CG303FQFE8/1", seqs);
char *sqans = "AAATACGGGTAGATATACCGCCATGTCTCGCAAACAGCCTCATCATGCCGCGCCTGCCCACTTTTTTGCATCAGTATCCCGGCATTGCGCTGGAACTTTGTAGTAGCGATCGACAGGTCGATTTACTACGGGAAGATTTCGACTGCGTGGTGCGCACAGAGCCGCTACATGCGCCAGGGATACTGACGCGCCCGCTTGGCAAACTGAGAAGAGTGAACTGCGCCAGCCCACAATACCTGGCGCGCTTTGGGTAATCCAGAAAAACCTTGACGATCTCGCCTCACATGCGGTGGTGCATTATTCATTGACCCCGGGAGTTTCTTCACCGGGTTTTGCCTTTGAAACTCCCACGGTATGCAGTGGTAAAAAACCGGCGGAAATGCTAACGGTAAACAGTACGAGACTTGGCATACAGCCTG";
char *quans = "@@@DDDDDFFFIIIIIIIIIIIIIIIIIIIIHHHIIFDDHHHHHHHHHHHHHFFFFFFFFF666666FFFFFFFFFFFFFCCADDDFDDCDDDDDD???6388CFFCCCCCDFFFFFDFFFF??8638<FF?AA>DFFFAA<<<FFFFFAACCFF???CFDDDDBBBBBBA<<889;888<<===BBBBB=;;A688<<9...3<4434443<<AAAAA??A==<>8624/2642..028>=<9989<<;4/..6;;<:,,,--..<<==:9<<<A<4444<=<<733224000<><8::CGGDDDDB::99400/0444322576;622....266666<68899444:8A?\?\?=>>>:3//.------55--266...3777666646...6297...269766///3:<><>;;93";
if (sq == NULL) {
fprintf(stderr, "Bugger, no sequence for @GFH7CG303FQFE8/1\n");
error++;
}
if (strcmp(sq, sqans)) {
error++;
printf("The sequence we retrieved for @GFH7CG303FQFE8/1 appeared to be wrong:\n%s\n", sq);
}
sq = get_sequence("NOSEQ", seqs);
if (sq != NULL) {
fprintf(stderr, "Using ID NOSEQ we retrieved %s\n", sq);
error++;
}
char *qual = get_quality("@GFH7CG303FQFE8/1", seqs);
if (strcmp(qual, quans)) {
fprintf(stderr, "The quality scores for @GFH7CG303FQFE8/1 do not appear correct\n");
error++;
}
qual = get_quality("NOSEQ", seqs);
if (qual != NULL) {
fprintf(stderr, "Got %s as quality scores for NOSEQ but shouldn't find any!\n", qual);
error++;
}
char *info = get_seq_information("@GFH7CG303FQFE8/1", seqs);
if (strcmp("@GFH7CG303FQFE8/1 length=419 xy=2234_0770 region=3 run=R_2010_04_12_12_22_54_", info)) {
printf("TEST: The information for @GFH7CG303FQFE8/1 was unexpected: '%s'\n", info);
error++;
}
if (error)
fprintf(stderr, "There were %d errors when running the tests\n", error);
else
fprintf(stderr, "All tests passed\n");
exit(error);
}
audio_encoder_settings_ptr audio_encoder_settings::duplicate() const
{
return audio_encoder_settings_ptr( new audio_encoder_settings(
new audio_encoder_settings::Impl( get_mode(), get_bit_rate(), get_quality() )
) );
}
int main(int argc,char *argv[])
{
void *handle;
option_t opt;
void* csi_attr;
int restart = 0;
RegisterSigint();
memset(&opt, 0, sizeof(option_t));
opt.ev = 6;
opt.sharpness = 1;
strcpy(opt.outpath, "./");
if (0 > parse_command(argc, argv, &opt))
return -1;
dc_pipe_init();
// opt.raw = 1;
start:
g_bQuit = 0;
restart = 0;
gp_IPC_VStream_Open(IPC_COLOR_YUYV, 0, 0, ON2_JPG);
csi_attr = gp_IPC_VDev_Open(NULL);
gp_IPC_VDev_Set_Exposure(csi_attr, opt.ev);
set_sharpness(csi_attr, opt.sharpness);
set_awb(csi_attr, opt.white_balance);
set_color(csi_attr, opt.color);
set_iso(csi_attr,opt.iso);
gp_IPC_Enable_Display(1, 0, IPC_SCALE_BILINEAR, (opt.width == 1920) ? 0:1);
gp_IPC_Enable_TimeStamp(opt.time_stamp);
dc_pipemsg_send(CMD_READY_KEY, 0, NULL);
while(1)
{
unsigned int msgId;
void* msgPara;
unsigned int mode;
if (g_bQuit)
break;
if(dc_pipemsg_receive(&msgId, &msgPara) > 0)
{
printf("msgId=%d\n", msgId);
if (msgPara)
{
mode = *(unsigned int*)msgPara;
printf("mode = %d\n", mode);
}
switch(msgId)
{
case CMD_DO_CAPTURE:
if(opt.raw)
{
gp_IPC_VDev_Close(csi_attr);
gp_IPC_VStream_Close();
gp_IPC_VStream_Open(IPC_COLOR_RAW, 0, 0, ON2_JPG);
csi_attr = gp_IPC_VDev_Open(NULL);
snap_shot(opt.width, opt.height, opt.quality, opt.outpath, opt.sequence, 1);
restart = 1;
g_bQuit = 1;
dc_response_cmd(msgId);
}
else
snap_shot(opt.width, opt.height, opt.quality, opt.outpath, opt.sequence, 0);
break;
case CMD_SET_DC_RESOLUTION:
get_resolution(mode, &opt.width, &opt.height);
gp_IPC_Enable_Display(0,0,0,0);
gp_IPC_Enable_Display(1, 2, IPC_SCALE_BILINEAR, (opt.width == 1920) ? 0:1);
break;
case CMD_SET_QUALITY:
opt.quality = get_quality(mode);
break;
case CMD_SET_EXPOSURE:
gp_IPC_VDev_Set_Exposure(csi_attr, mode);
break;
case CMD_SET_SHARPNESS:
set_sharpness(csi_attr, mode);
break;
case CMD_SET_AWB:
set_awb(csi_attr, mode);
break;
case CMD_SET_COLOR:
set_color(csi_attr, mode);
break;
case CMD_SET_ISO:
set_iso(csi_attr, mode);
break;
case CMD_SET_DC_DATE_STAMP:
opt.time_stamp = mode;
gp_IPC_Enable_TimeStamp(opt.time_stamp);
break;
case CMD_SET_SEQUENCE:
opt.sequence = mode ? 3:0;
break;
case CMD_SET_ZOOM:
mode = mode ? mode + 10: 0;
gp_IPC_Set_Zoom(mode);
break;
case CMD_SET_EXIT:
g_bQuit = 1;
break;
}
if (!g_bQuit)
dc_response_cmd(msgId);
}
}
printf("++++++++++dc exit++++++++++\n");
gp_IPC_VDev_Close(csi_attr);
gp_IPC_VStream_Close();
if(restart)
goto start;
dc_response_cmd(CMD_SET_EXIT);
}