/*! Called at the end of the pileup.
*/
void coverage_output::at_target_end(const uint32_t tid) {
char* refseq = get_refseq(tid); // reference sequence for this target
uint32_t pos = target_length(tid)+1;
if (m_read_begin_output.is_open()) {
// catches this position
for (uint32_t j=m_last_position_1+1; j<pos; j++) {
if (j>=3) {
std::string read_begin_s;
for (int i=1; i<=3; i++) {
read_begin_s += complement_base_char(reference_base_char_1(tid, j-i+1));
}
m_ref_begin_bot_bins[read_begin_s]++;
}
if (j<target_length(tid)-3) {
std::string read_begin_s;
for (int i=1; i<=3; i++) {
read_begin_s += reference_base_char_1(tid, j+i-1);
}
m_ref_begin_top_bins[read_begin_s]++;
}
}
m_read_begin_output << "base_1\tbase_2\tbase_3\tread_top\tread_bot\tref_top\tref_bot" << std::endl;
for (int b1=0; b1<base_list_size-1; b1++) {
for (int b2=0; b2<base_list_size-1; b2++) {
for (int b3=0; b3<base_list_size-1; b3++) {
std::string key_s;
key_s += base_char_list[b1];
key_s += base_char_list[b2];
key_s += base_char_list[b3];
uint32_t read_begin_top_count=0;
if (m_read_begin_top_bins.find(key_s) != m_read_begin_top_bins.end()) {
read_begin_top_count = m_read_begin_top_bins[key_s];
}
uint32_t read_begin_bot_count=0;
if (m_read_begin_bot_bins.find(key_s) != m_read_begin_bot_bins.end()) {
read_begin_bot_count = m_read_begin_bot_bins[key_s];
}
uint32_t ref_begin_top_count=0;
if (m_ref_begin_top_bins.find(key_s) != m_ref_begin_top_bins.end()) {
ref_begin_top_count = m_ref_begin_top_bins[key_s];
}
uint32_t ref_begin_bot_count=0;
if (m_ref_begin_bot_bins.find(key_s) != m_ref_begin_bot_bins.end()) {
ref_begin_bot_count = m_ref_begin_bot_bins[key_s];
}
m_read_begin_output << base_char_list[b1] << "\t" << base_char_list[b2] << "\t" << base_char_list[b3]
<< "\t" << read_begin_top_count << "\t" << read_begin_bot_count << "\t" << ref_begin_top_count << "\t" << ref_begin_bot_count<< std::endl;
}
}
}
}
}
void eapol_am_wlan_authentication_symbian_c::ReadWPASettingsL()
{
EAP_TRACE_BEGIN(m_am_tools, TRACE_FLAGS_DEFAULT);
EAP_TRACE_DEBUG(
m_am_tools,
TRACE_FLAGS_DEFAULT,
(EAPL("eapol_am_wlan_authentication_symbian_c::ReadWPASettingsL(): %s, this = 0x%08x => 0x%08x\n"),
(m_is_client == true) ? "client": "server",
this,
dynamic_cast<abs_eap_base_timer_c *>(this)));
EAP_TRACE_RETURN_STRING(m_am_tools, "returns: eapol_am_wlan_authentication_symbian_c::ReadWPASettingsL()");
eap_status_e status(eap_status_ok);
if (m_selected_eapol_key_authentication_type == eapol_key_authentication_type_WPS)
{
EAP_TRACE_DEBUG(
m_am_tools,
TRACE_FLAGS_DEFAULT, (EAPL("WPS does not use CommDbIf anymore.\n")));
return;
}
TIndexType index_type(ELan);
TUint index(0UL);
status = read_database_reference_values(
&index_type,
&index);
if (status != eap_status_ok)
{
EAP_TRACE_END(m_am_tools, TRACE_FLAGS_DEFAULT);
User::Leave(m_am_tools->convert_eapol_error_to_am_error(EAP_STATUS_RETURN(m_am_tools, status)));
}
if (index_type == ELan)
{
EAP_TRACE_DEBUG(
m_am_tools,
TRACE_FLAGS_DEFAULT,
(EAPL("WLAN settings: m_WPA_override_enabled=%d\n"),
m_WPA_override_enabled));
EAP_TRACE_DATA_DEBUG(
m_am_tools,
TRACE_FLAGS_DEFAULT,
(EAPL("m_wpa_preshared_key"),
m_wpa_preshared_key.get_data(),
m_wpa_preshared_key.get_data_length()));
EAP_TRACE_DATA_DEBUG(
m_am_tools,
TRACE_FLAGS_DEFAULT,
(EAPL("m_SSID"),
m_SSID.get_data(),
m_SSID.get_data_length()));
// Get WPA pre shared key & SSID
if (m_is_client == true
&& (m_selected_eapol_key_authentication_type == eapol_key_authentication_type_RSNA_PSK
|| m_selected_eapol_key_authentication_type == eapol_key_authentication_type_WPA_PSK))
{
TPSKEntry pskEntry;
pskEntry.indexType = index_type;
pskEntry.index = index;
pskEntry.ssid.Zero();
pskEntry.password.Zero();
pskEntry.psk.Zero();
TInt error(KErrNone);
// Retrieve saved PSK only when override is not in effect
TRAP(error, RetrievePSKL(pskEntry));
if (error != KErrNone
|| m_SSID.compare(pskEntry.ssid.Ptr(), pskEntry.ssid.Size()) != 0
|| m_wpa_preshared_key.compare(pskEntry.password.Ptr(), pskEntry.password.Size()) != 0)
{
// No previous PSK or parameters were changed.
// We need to calculate PSK again
EAP_TRACE_DEBUG(m_am_tools, TRACE_FLAGS_DEFAULT, (EAPL("No previous PSK found...\n")));
crypto_wpa_psk_password_hash_c password_hash(m_am_tools);
if (m_wpa_preshared_key.get_data_length() == 2ul*EAPOL_WPA_PSK_LENGTH_BYTES)
{
// This is hex ascii 64-digit WWPA-PSK.
// Convert it to 32 octets.
u32_t target_length(EAPOL_WPA_PSK_LENGTH_BYTES);
status = m_wpa_preshared_key_hash.set_buffer_length(EAPOL_WPA_PSK_LENGTH_BYTES);
if (status != eap_status_ok)
{
send_error_notification(eap_status_key_error);
EAP_TRACE_END(m_am_tools, TRACE_FLAGS_DEFAULT);
User::Leave(m_am_tools->convert_eapol_error_to_am_error(EAP_STATUS_RETURN(m_am_tools, status)));
}
status = m_wpa_preshared_key_hash.set_data_length(EAPOL_WPA_PSK_LENGTH_BYTES);
if (status != eap_status_ok)
{
send_error_notification(eap_status_key_error);
EAP_TRACE_END(m_am_tools, TRACE_FLAGS_DEFAULT);
User::Leave(m_am_tools->convert_eapol_error_to_am_error(EAP_STATUS_RETURN(m_am_tools, status)));
}
status = m_am_tools->convert_hex_ascii_to_bytes(
m_wpa_preshared_key.get_data(m_wpa_preshared_key.get_data_length()),
m_wpa_preshared_key.get_data_length(),
m_wpa_preshared_key_hash.get_data(EAPOL_WPA_PSK_LENGTH_BYTES),
&target_length);
if (status != eap_status_ok
|| target_length != EAPOL_WPA_PSK_LENGTH_BYTES)
{
send_error_notification(eap_status_key_error);
EAP_TRACE_END(m_am_tools, TRACE_FLAGS_DEFAULT);
User::Leave(m_am_tools->convert_eapol_error_to_am_error(EAP_STATUS_RETURN(m_am_tools, status)));
}
}
else
{
status = password_hash.password_hash(
&m_wpa_preshared_key,
&m_SSID,
&m_wpa_preshared_key_hash,
0,
0);
if (status != eap_status_ok)
{
send_error_notification(eap_status_key_error);
EAP_TRACE_END(m_am_tools, TRACE_FLAGS_DEFAULT);
User::Leave(m_am_tools->convert_eapol_error_to_am_error(EAP_STATUS_RETURN(m_am_tools, status)));
}
}
EAP_TRACE_DATA_DEBUG(
m_am_tools,
TRACE_FLAGS_DEFAULT,
(EAPL("new WPA-PSK SSID"),
m_SSID.get_data(),
m_SSID.get_data_length()));
EAP_TRACE_DATA_DEBUG(
m_am_tools,
TRACE_FLAGS_DEFAULT,
(EAPL("new WPA-PSK preshared key"),
m_wpa_preshared_key.get_data(),
m_wpa_preshared_key.get_data_length()));
EAP_TRACE_DATA_DEBUG(
m_am_tools,
TRACE_FLAGS_DEFAULT,
(EAPL("new WPA-PSK hash"),
m_wpa_preshared_key_hash.get_data(),
m_wpa_preshared_key_hash.get_data_length()));
// Save new PSK.
pskEntry.ssid.Copy(
m_SSID.get_data(),
m_SSID.get_data_length()
);
pskEntry.password.Copy(
m_wpa_preshared_key.get_data(),
m_wpa_preshared_key.get_data_length()
);
pskEntry.psk.Copy(
m_wpa_preshared_key_hash.get_data(),
m_wpa_preshared_key_hash.get_data_length()
);
EAP_TRACE_DEBUG(m_am_tools, TRACE_FLAGS_DEFAULT, (EAPL("Saving PSK.\n")));
SavePSKL(pskEntry);
}
else
{
// Copy retrieved WPAPSK hash to member variable
status = m_wpa_preshared_key_hash.set_copy_of_buffer(pskEntry.psk.Ptr(), pskEntry.psk.Size());
if (status != eap_status_ok)
{
send_error_notification(eap_status_key_error);
EAP_TRACE_END(m_am_tools, TRACE_FLAGS_DEFAULT);
User::Leave(m_am_tools->convert_eapol_error_to_am_error(EAP_STATUS_RETURN(m_am_tools, status)));
}
EAP_TRACE_DATA_DEBUG(
m_am_tools,
TRACE_FLAGS_DEFAULT,
(EAPL("old WPA-PSK SSID"),
m_SSID.get_data(),
m_SSID.get_data_length()));
EAP_TRACE_DATA_DEBUG(
m_am_tools,
TRACE_FLAGS_DEFAULT,
(EAPL("old WPA-PSK preshared key"),
m_wpa_preshared_key.get_data(),
m_wpa_preshared_key.get_data_length()));
EAP_TRACE_DATA_DEBUG(
m_am_tools,
TRACE_FLAGS_DEFAULT,
(EAPL("old WPA-PSK hash"),
m_wpa_preshared_key_hash.get_data(),
m_wpa_preshared_key_hash.get_data_length()));
}
}
}
else
{
// At the moment only LAN bearer is supported.
User::Leave(KErrNotSupported);
}
EAP_TRACE_END(m_am_tools, TRACE_FLAGS_DEFAULT);
}
